Rarities aren't screwed up - but some have changed with time...
Most got rarer with time, but some (like Counterspell) got more common.
The only thing I recall reading was that there were some Mountains which showed up in boosters because they had one as a filler card to the sheet of commons since they were one common short.
Also, CoP: Black wasn't in Alpha, but it made it into Beta. I thought one of the Dual Lands wasn't in either, but Gatherer shows all 10, and so does Apprentice.
Oh, and I have a Deck ready - if anyone else is ready...