I see satchel pointed out the Moose Haas problem - he had a great season in everything but giving up hits (
), which meant he gave up a ton of runs. OOTP discounts that and sees a 3.00-3.50 ERA type pitcher.
The other big thing is historical stadiums. Essentially, Brooks Robinson was the example I always used for my '69 league. Brooks had 10-15 homers a year power, but Memorial Stadium made that more like 20-25 homer power. OOTP imports a 20-25 homer player as it doesn't account for parks, and then sticks him in Memorial Stadium, where he becomes a 30-35 homer player!