Hey there. I dunno if you wanted to just report a bug, or if it was a problem for you, but I know how to fix it. If you reverse the tags (put indent first, and then sub) it fixes the overlapping issue. For example:

[noparse][indent][sub]This is an example.[/sub][/indent][/noparse]

equals:
[indent][sub]This is an example.[/sub][/indent]

Just thought you might wanna know :)