Plot hole: They found seminal fluid left in Caroline Polhemus. Why didn't they subject it to DNA testing, which would have been a powerful indicator of Sabich's guilt? Fertility (or otherwise) has nothing to do with it - as well as non-motile sperm (which contain DNA anyway) the seminal fluid would contain discarded skin and blood calls in abundance. DNA testing was first used in a criminal case in 1985 and was in fairly common use by 1988.
Other mistake: When Harrison Ford returns to the crime scene to search for "evidence" we see blood stains on the carpet, which has been on the carpet for days. The blood is bright red and shows no signs of coagulation, but blood turns dark red when it coagulates after only a few hours.
Factual error: Tommy Molto stands up and tells Judge Lyttle that the prosecution has not been able to find a key piece of evidence: a bar glass found in the victim's apartment. The jury is present when Molto makes this statement. That would never happen in a real courtroom. The judge had not yet decided whether testimony about the glass could be offered by the prosecution, so he certainly would not want the jury to hear anything about the glass until AFTER he made that decision.
Continuity mistake: When Harrison Ford receives a small stack of photos showing the victim bound, he looks through them and evens them against the desk while he is being told about the pictures. It cuts to him picking up the same stack of photos and evening them into a pile again, but his left hand was on his lap and he needed to bring it up and over to pick up the photos, when he was just holding them.
Factual error: Judge Lyttle holds several private discussions with the lawyers outside of chambers without having a court reporter present. A court reporter would always be present in such situations. The point of those private discussions is to prevent the jury from overhearing them, but they are still on the record.
Continuity mistake: About 35 minutes in, Rusty and Raymond are in the latter's office, drinking White Label scotch. During the scene, Raymond pours himself another drink and replaces the bottle on the desk in a slightly different position. In the next shot, the bottle is back in exactly the same position as it was earlier and before Raymond picked it up.