There is ~1.3ms delay between what is heard from the headphones and what is actually recorded. That means if you have perfect timing, and play a note at the exact time it is played back, the Zoom R16 will incorrectly place it around 1.3ms in the future on the track you're recording to. When you play the resulting recordings, there will be a 1.3ms gap between what is recorded on track 1 and track 2.
The Zoom R16 is worse than the Fostex MR-8 MkII which has .79ms delay between recorded tracks. Does it matter? For most cases probably not. But if you recorded with a PC you'd have a 0ms delay between tracks because the software automatically compensates for the delay by offsetting the recording on the timeline. Why hardware multitrack recorders don't do this is probably some technical limitation or laziness.