Final Cut Pro cuts audio last split second in clips when importing

Could it possibly be caused by the sample rate of the recorded audio being different from that of the project?

Audio is often recorded at 44.1kHz whereas by default FCP X seems to use 48kHz.

A google search will show that this problem also occurs in Premiere.

I'm far more curious as to why they cut your program into little pieces in the first place... if I had to guess, they recorded to a drive formatted FAT32 and the filesystem just couldn't handle anything bigger. Which would be stupid on their part, and a good reason to never hire them again, never mind them telling you to use Premiere (barf).

I have seen instances where a small no-audio tail on a clip that was auto-split during recording could be trimmed. The few times I've seen it, the tail was just a repeated frame. Once trimmed, the audio ends up almost matching, but with a pop or click at the edit point.

The pop or click is very common in audio editing as it’s difficult to get the cut on the crossover point. Normally a quick cross fade is used. The FCP cross fade defaults to a very short duration for just this purpose.

Quite true. With video files that have been auto-split, there's not much you can do to fix it as there are no handles (and frequently a missing frame or two of audio).

With a separate, complete audio recording, OP could try to patch the gaps with good audio, and fudge the picture to cover the gap. Haven't seen any indication that such a recording exist in this case, but that was how I managed to fix those instances.

Open ine of those affected clips in Quicktime Player. Does the audio go all the way to the end?

Is the silent bit just one frame or more? (Expand the timeline so you can see individual frames).

I am also wondering whether it could be anything to do with the compression and Long GOPs of the video.

Have you tried converting to ProRes?