Updated category to Any%, didn't realize I submitted it to the wrong category until just now. Sorry!
In the mission "A Way In" it is possible to confuse the game and collect a checkpoint before it loads in if you get a very fast takedown on the thief (0:42 in the run shown). If the checkpoint is collected early like it is here, the rest of the mission progresses as normal but with the previous checkpoint being loaded onto the minimap and in-game during the final chase segment as well as Vinny saying lines from the thief chase for a while.
Additionally, if you were to restart mission after both checkpoints have loaded, instead of starting at the very beginning of the mission like usual, it starts you right after taking down the thief and before the final chase (pretty sure this isn't normal but didn't check yet). Although this does act as a "checkpoint" of sorts, it also keeps consistent timing as if you never restarted and just collected the checkpoint the first time. As a result, there is no opportunity for any kind of checkpoint skipping unfortunately.
Last for the night! Sorry for the late upload, timing took longer than expected lol