I've repressed my Naptan memories! :P

If the errors are specific for York, I suspect their data in Naptan has/had issues. It's each local authorities responsibility to update Naptan, and I'm sure some are worse than others.

Taking a look at another website that shows Naptan data:
https://www.geopunk.co.uk/bus-stop/3290YYA00260
https://www.geopunk.co.uk/bus-stop/3290YYA00261
We can see that both of these have the same NaptanCode (3290026), I suspect the first should 32900260 and the latter 32900261.

I can't find any details about deps.at, but Naptan doesn't include timetable information. It may be getting it's data via Traveline or the new(ish) BODS. It seems likely that there is an issue in Naptan, but not the other dataset.