This was true of the real book too. Quite a lot of the songs have incorrect transcriptions, sometimes they use a different key than the original, or the "original" key when a different one is more commonly heard. All editions of it I've seen have this to a significant extent, of course with differences making it even more confusion sometimes.
And a lot of natural variation has been elided with these tools, a lot of jazz classics I'm pretty sure didn't really have a "standard" version until after the real book took over; different fake books were popular in different cities and so there was regional performance variation that we don't see much of anymore.
There are probably novel issues introduced by the ireal fakes but a lot of them are the same problems my grandfather was observing as a young working musician when the real book became so dominant. They are extremely real downsides of these tools though.