In the Pilot, when Jack and Will are playing cards with two other guys, Will deals Jack his first card two times between shots.
In "Cheaters" Will's father takes several sips from his drink during the intermission of a musical, but the level in his glass never changes between shots.
In "Boo Humbug", Harlin's daughter takes her bumblebee mask with her when she leaves. A few shots later, when Grace and Will dive for the candy, it is on the coffee table again.
In episode 1:12, "My Fair Maidy", when Will introduces Grace to April, the pens in Grace's hair changes between shots.
The layout of Will's apartment, specifically his bedroom and the bathroom(s), don't match up with the layout of the hallway outside his door.
In the series, Will's apartment has a balcony, but the outside shot of the building shows no balconies. In fact, the actual building at 155 Riverside Drive has no balconies.
In the earlier series, the deadlock on Grace's office door is backwards. The door opens inwards yet the part of the lock where the key is required is on the inside of the office and the latch that can be opened by hand is on the outside - rendering the lock useless. This is corrected in later seasons.
Actor Eric McCormack is Canadian. Will, the character he plays, is not. Nonetheless throughout the series "Will" frequently lets slip with a Canadian accent, particularly on the stereotypical 'about', which he pronounces 'aboot'.