Look of course Arsenal have benefitted from leniency on wwe style corners etc and the fact that they have managed to get this far without a red is wild. I'm not sure about penalties. I don't recall any that blatantly should have been given against them but I don't watch many of their games as they bore me to death. The one last week for all the furore could have gone either way and as usual this season the refs just ignore wrestling in the box. It's not restricted to Arsenal either, just look at what that little rat Bernardo Silva gets away with each week.
But to suggest it's a conspiracy from the top is akin to suggesting the moon landing was faked. It's just a bit silly to me. The PL PGMOL and the refs themselves would all have to be involved. I can't see them all getting together and deciding to go easy on Arsenal (for reasons that have yet to be properly explained as far as I can see).
However, there's always the possibility that Arsenal would be preferred to City, because of the charges or to change things up etc and that this attitude is bleeding into how they're being refereed, on a sort of subconscious level.