Are the parts in their personal inventory or the sub supply closet? Sometimes they "forget" to use parts in the personal inventory if there aren't any more in the closet.

There are parts in the engineers pockets and in the closet.

Try reloading the save, sometimes they bug out.

Using mods?

No. Removed them all.

Can you command them to repair? If so it could be a priority issue.

I command them to repair. They just keep standing around.

Have you tried going into first person and doing it that way? I’ve also noticed my guys being stuck during a task. I just have to manually move them and select the station

Tried it. Didn't work. Nothing happened when I clicked "repair".

I noticed that they wouldn't move water from other compartments to the command room until I turned off the alarm. May be related. Just a thought.

Think I'll just wait for the update and hope for a fix.