I haven’t seen any known issues with the USB-C/Thunderbolt ports. This thread was about the issues related to the software issues with Big Sur negotiating certain resolutions over certain ports, which seems to have been substantively resolved in 11.2.
Assuming you are saying the negotiated link speed of your CalDigit to your Internet router drops to 100mbps, the most common cause of this is your network cable. You could try swapping this. If you aren’t sure if it was your link speed or not, note the color of your network connection light for the network port your connected to and then note it again the next time it drops to 100. If the colour changes then you have a network port/cable link speed issue and can try another cable... or if the issue happens enough, just try a new cable and see if it resolves it.
Since you are using the Mac Mini, when that happens, try switching your connection from your internet modem to your Mac Mini instead of your CalDigit to see if the problem persists.
If this doesn’t help, suggest you start a new thread to see if others have a similar problem.