M1Pro MacBook Pro upgraded to Monterey 12.5.1, now has major issues

Revive or restore a Mac with Apple silicon using Apple Configurator

If this is not possible due to lack of secondary apple computer ( as per info contained in above link ) or not within your skill set

Apple Repair and choose the method best suited for your needs. The On Hands method by Apple Experts maybe able to put the computer back to working order

Point one- " (dock icons showing up again when previously removed from said dock) " refer to below image for illustration

Point two - " some apps don't open again after initially working ."

Not know what specific applications are involved - this is a bit of Mind Reading exercise which I am not good at.

The next best thing for us to having a semi - actual On-Hand experience  with this computer is to follow the steps below

Download the Application Etrecheck directly from the Developer. 

The application is free or paid from added features. 

It will take a Snap Shot -  both the hardware and software.

 The Report will Not Reveal Any Personal Information. 

Post back the Full Report - copy and paste - using the Additional Text Icon ( 3rd Icon to last )

We can have a look at the report for possible issues and may have possible suggestions to resolve the issues.

That is a lot of work and trouble shooting you have done 👍 but a quick question.

Once the drive had been wipe and a fresh installation was performed, was Setup Assist used to Restore all your data, application etc back into the computer ?

Issues that may have exist when the TM Backup was performed will be migrated to the New Installation This would effectively Negate all the work that has been done ( Wipe and Clean Installation )

There might be a way to roll back to Monterey 12.5 but this is much more complicated and risky ( IMHO ) for Apple Silicon computer.

It is not like the " Olden Days " on Intel and make a Bootable Installer and Wipe the Entire Drive and lay down a new Installation.

Thank you for the Report.

I will dissect it, in detail,  and get back to you.

Going back to lower version of Monterey on an Apple Silicon Computer is not as easy as the Old Days with Intel Based Computers.

Creating a Bootable Installer of an older version of Monterey and booting into it on M1 / M2 computer and wiping the drive and installing - will not work - period

As per the supplied report, to be polite, have never seen a drive structure like this one let along on an M1 / M2 Apple Silicon Computer.

It looks to these old eyes, that there may have been several attempted or failed attempts to upgrade various versions of macOS Monterey

  MacBook Pro (16-inch, 2021)

  MacBook Pro Model: MacBookPro18,1

   Apple M1 Pro (m1) CPU: 10-core

  16 GB RAM - Not upgradeable

  Battery: Health = Normal - Cycle count = 149

Drives:

  disk0 - APPLE SSD AP0512R 500.28 GB (Solid State - TRIM: Yes) 

  Internal Apple Fabric NVM Express

    disk0s1 [APFS Container] 524 MB

V -  disk1 [APFS Virtual drive] 524 MB (Shared by 4 volumes)

P - disk1s1 - iSCPreboot (APFS) [APFS Preboot] (8 MB used)

        disk1s2 - xART (APFS) (6 MB used)

        disk1s3 - Hardware (APFS) (3 MB used)

R - disk1s4 - Recovery (APFS) [Recovery] (20 KB used)

    disk0s2 [APFS Container] 494.38 GB

V -  disk3 [APFS Virtual drive] 494.38 GB (Shared by 6 volumes)

disk3s1 - Macintosh HD - Data (APFS) [APFS Virtual drive] (28.77 GB used)

        disk3s2 - Update (APFS) (60 MB used)

        disk3s3 (APFS) [APFS Container] (15.42 GB used)

          disk3s3s1 - Macintosh HD (APFS) [APFS Snapshot] (15.42 GB used)

 P - disk3s4 - Preboot (APFS) [APFS Preboot] (408 MB used)

 R - disk3s5 - Recovery (APFS) [Recovery] (822 MB used)

 V - disk3s6 - VM (APFS) [APFS VM] (20 KB used)

    disk0s3 [APFS Container] 5.37 GB

V - disk2 [APFS Virtual drive] 5.37 GB (Shared by 2 volumes)

R - disk2s1 - Recovery (APFS) [Recovery] (1.71 GB used)

        disk2s2 - Update (APFS) (295 KB used)

Count 4 Virtual 

Count 2 Preboot

Count 3 Recovery

1 - Terminal command

diskutil list

/dev/disk0 (internal):

   #:                       TYPE NAME                    SIZE       IDENTIFIER

   0:      GUID_partition_scheme                         251.0 GB   disk0

   1:             Apple_APFS_ISC ⁨⁩                        524.3 MB   disk0s1

   2:                 Apple_APFS ⁨Container disk3⁩         245.1 GB   disk0s2

   3:        Apple_APFS_Recovery ⁨⁩                        5.4 GB     disk0s3

/dev/disk3 (synthesized):

   #:                       TYPE NAME                    SIZE       IDENTIFIER

   0:      APFS Container Scheme -                      +245.1 GB   disk3

                                 Physical Store disk0s2

   1:                APFS Volume ⁨Macintosh HD⁩            15.4 GB    disk3s1

   2:              APFS Snapshot ⁨com.apple.os.update-...⁩ 15.4 GB    disk3s1s1

   3:                APFS Volume ⁨Preboot⁩                 815.0 MB   disk3s2

   4:                APFS Volume ⁨Recovery⁩                804.7 MB   disk3s3

   5:                APFS Volume ⁨Data⁩                    17.1 GB    disk3s5

   6:                APFS Volume ⁨VM⁩                      20.5 KB    disk3s6

2 - Terminal command

diskutil apfs list

p.phillips@Ps-Mac-Mini-M1 ~ % diskutil apfs list

APFS Containers (3 found)

|

+-- Container disk3 700BD137-794A-4752-AA66-B67FC6606651

    ====================================================

    APFS Container Reference:     disk3

    Size (Capacity Ceiling):      245107195904 B (245.1 GB)

    Capacity In Use By Volumes:   34250821632 B (34.3 GB) (14.0% used)

    Capacity Not Allocated:       210856374272 B (210.9 GB) (86.0% free)

    |

    +-< Physical Store disk0s2 BD6C28FC-DEA8-440D-9BC3-55545C0E0531

    |   -----------------------------------------------------------

    |   APFS Physical Store Disk:   disk0s2

    |   Size:                       245107195904 B (245.1 GB)

    |

    +-> Volume disk3s1 BA865CB6-0363-4DAA-9E62-BBB34002CC61

    |   ---------------------------------------------------

    |   APFS Volume Disk (Role):   disk3s1 (System)

    |   Name:                      Macintosh HD (Case-insensitive)

    |   Mount Point:               Not Mounted

    |   Capacity Consumed:         15415513088 B (15.4 GB)

    |   Sealed:                    Yes

    |   FileVault:                 No (Encrypted at rest)

    |   |

    |   Snapshot:                  1FD4ACB2-DC25-4077-A2D4-0F4B1F5E4FE4

    |   Snapshot Disk:             disk3s1s1

    |   Snapshot Mount Point:      /

    |   Snapshot Sealed:           Yes

    |

    +-> Volume disk3s2 552DE671-42B4-4373-9860-5A928A6B01E9

    |   ---------------------------------------------------

    |   APFS Volume Disk (Role):   disk3s2 (Preboot)

    |   Name:                      Preboot (Case-insensitive)

    |   Mount Point:               /System/Volumes/Preboot

    |   Capacity Consumed:         814952448 B (815.0 MB)

    |   Sealed:                    No

    |   FileVault:                 No

    |

    +-> Volume disk3s3 F489BBDF-05E3-47E2-960C-F9DB245DC360

    |   ---------------------------------------------------

    |   APFS Volume Disk (Role):   disk3s3 (Recovery)

    |   Name:                      Recovery (Case-insensitive)

    |   Mount Point:               Not Mounted

    |   Capacity Consumed:         804651008 B (804.7 MB)

    |   Sealed:                    No

    |   FileVault:                 No

    |

    +-> Volume disk3s5 1460D985-958A-4A68-9CD3-21CB0C423F02

    |   ---------------------------------------------------

    |   APFS Volume Disk (Role):   disk3s5 (Data)

    |   Name:                      Data (Case-insensitive)

    |   Mount Point:               /System/Volumes/Data

    |   Capacity Consumed:         17059266560 B (17.1 GB)

    |   Sealed:                    No

    |   FileVault:                 No (Encrypted at rest)

    |

    +-> Volume disk3s6 1D8585AD-3662-4A00-BC64-AE009704EB3F

        ---------------------------------------------------

        APFS Volume Disk (Role):   disk3s6 (VM)

        Name:                      VM (Case-insensitive)

        Mount Point:               /System/Volumes/VM

        Capacity Consumed:         20480 B (20.5 KB)

        Sealed:                    No

        FileVault:                 No

Excellent work 👍 and Bravo well done 😀

You are welcome and thank you too 🇨🇦

Do come back to the Apple Support Communities ( ASC )  in the future, if / or when additional questions may arise