I noticed a quirk with the transpose function. If you try to transpose something without anything selection, the tracker automatically selects seemingly random sections in the pattern area. This happens with the Ctrl+F1/F2/F3/F4 combination as well as the Ctrl+Mousewheel combination (and also affects Shift+Mousewheel).
It's not a huge problem most of the time, but sometimes you can end up accidentally transposing something you didn't intend to transpose.
I ran into this myself and noticed how the selection is not (technically) random but actually from the cursor to the endpoint of the previous selection.
So if you made a selection from point A to point B, then move the cursor to location C and try to transpose without a new selection, FT imposes a selection from C to B (instead of C to C). Whoops!