In "No Chris Left Behind", the Morningwood Academy sign has "NO IRISH" crossed out and "IRISH OK" written under it. The next time we see the sign, there is no trace whatsoever of either line of the Irish text.
When shown a quick view of Cleveland's House it is one and a half story Cape Cod house, like Peter's House. But, whenever Peter does one of his "Shenanigans' near Cleveland's house, it is a full two story, non-Cape Cod home.
Peter lives in a Cape Cod house. They have one full floor and an upstairs which has slanted walls. When there are screen shots of Peter's room, Chris's room, Stewie or Meg's room, they have straight walls.
The most frequent animation error seen in the show is the appearance of the eyebrows (and some cases the eyes). The eyebrows are known to disappear and/or reappear at times, or in rare cases even "duplicate", creating an extra pair of eyebrows (as seen on Lois' father when Peter meets him in "Death Lives").
Peter's shirt buttons the wrong way. Men's shirts button with the left side over the right side, but Peter's shirt is backwards, in the same direction as Lois's shirt. Occasionally, but very rarely, this changes.