I was having a similar-sounding problem on my MBA (June 2013, 1.3 gHz, 8gb ram) not long after I upgraded from to 10.12.3. I'd open an application, it would work for a time then freeze, sometimes with the spinning beachball sometimes not, sometimes I could command-tab back to finder, but sometimes not, but the OS would let me force-quit so I'd have to force restart the computer. I thought a clean reinstall would help but the computer kept getting stuck near the end of the installation process.
After 2 trips to the local Apple Store it seems to be fixed. Eventually, after the technician tried a new clean reinstall, the computer wouldn’t even see it’s own internal drive while booted into recovery mode, so they opened up the computer, cleaned out some dust, tried putting in a new drive, which recovery mode did recognise, Then they tried putting the original drive back in, and it worked too. So OS 10.12.3 reinstalled successfully, the applications that were freezing before now work. It’s been a few weeks now and I haven’t had any trouble with freezing. Sorry this isn’t a definitive solution, maybe there was dust inside the connector between the SSD and the logic board causing an intermittent fault, that only coincidentally started when I upgraded to 10.12? The Apple technician couldn’t say for certain what happened.