I had two problems caused by transmission replacement, both of which required the car being towed (and are documented elsewhere in the forums). First issue was the shift cable became detached. Second issue was the car becoming comatose after parking; it would neither turn on nor turn off! Both problems showed up within a couple of months following replacement and were promptly fixed.
This was two years ago. New transmission has performed perfectly since then. So yes, there's cause for concern following major surgery, but nothing that can't be handled.