The "long second" device is supposed to stretch out 1 second of time to appear as 10 seconds. The first time, it lasts for some 90 seconds, and we see a bullet moving at well under 1 mph, indicating a reduction factor of much more than 10. The second time, the effect lasts for about 45 seconds.
When McNulty comes down the line into the body of his ancestor, a young girl, he claims that to reach Deth, he had to sneak around the parents. However, he fails to explain why he couldn't have jumped into one of the parents.
When Jack and Lena are travelling along Caheunga Blvd in the T-Bird after the shopping mall incident, it is obvious the car is on a trailer as they appear to be higher up than the passing traffic, including vans! Also, if you observe Jack's steering wheel actions which appear to be quite erratic at times, the car does not appear to copy his movements.
Near the start of the movie when Jack is shown a baseball card with Hap Ashby on he says '1963 Angels, what the hell is this?' if you look closely at the card there is no mention of the year 1963 so how would he have known the year?
The goof item below may give away important plot points.
The "murder" of one of the council members is caused by Whistler killing the man's ancestors. Chairman Spencer describes the man, as well as his descendants, as disappearing before his eyes. However, killing the man's ancestors should result in the man never having been born, meaning no one should have any memory of him ever having existed.