My key commands like shift+command click and drag are not working, as well as my alt+drag and more. It's almost like my inDesign is stuck in free transform and I haven't been able to figure out how to get it back to normal! Anyone else experiencing this issue?
Sorry to hear about the trouble you are facing. This generally happens when the third-party application is interfering with InDesign. In that case, you may try running the app inSafe Modeand launch InDesign only. Then, open the document, and try alt+drag to see if it is working or not. In Safe Mode, your system starts to perform certain checks and prevent third-party software/ services from automatically loading or opening. If it works fine in Safe Mode, then open other apps one by one, which you usually open, and see which app is conflicting with InDesign. You can check and find the culprit app/ process/ plugin/ extension with the help of Activity Monitor/Task Manager and then you'll have to close/ disable/ uninstall them on your user account and then launch the app in normal mode. I hope it helps!
Also, it can happen due to corrupt preferences. In that case, you may try resetting them as suggested above by@Mike Witherell.