I have found that when using Instrument tracks with a negative track delay time and rendering in place, when there is a note at the beginning of a MIDI clip, the beginning of the note gets cutoff in the resulting audio.
For example, if I program a MIDI note and Clip that starts on a downbeat and add a -100ms track delay, in the resulting bounce, the beginning of the note is cutoff. The resulting audio file created should start 100ms before the downbeat (accounting for the delayed first note), not on the downbeat, cutting off the beginning of the note.
The solution is to drag the beginning of the MIDI Clip to start earlier, but this is easy to forget to do, and would be great if it worked as expected.