I've checked the sequence settings and the clips I'm using and they all claim to be 23.976fps. The gaps don't happen right across the timeline, but it occassionally happens on a random few.
Have you applied some effect to the clips in your above image?
If not, the red line would indicate a mismatch between
your media frame rate and your sequence frame rate
(and it would explain occasional gaps).
The only alteration is the dimensions of the sequence - the source is 1920x1080 and the sequence is 1920x800 as the film is supposed to be anamorphic. The clips used to be in another sequence as they had gone through PluralEyes. Each scene has been edited in it's own sequence (all have a red line but no gaps) but now that they've all come together in one, these gaps have appeared.
The clips used to be in another sequence
That's how it happens. Copying from one sequence with one frame rate to another sequence with a different frame rate, you occasionally get these little 'between frame' cuts and gaps. The solution is not to put the clips in the wrong sequence to begin with. Once you have the gaps, you're only fix is to go through the sequence one edit at a time with the view expanded so you can see and manually fix the gaps by adjusting their In/Out points.
I would also recommend editing in a matching 1080 sequence and using the following: