Rhone left two officers to guard the Woodward house, when they left. Yet when they come back, only one is seen on the floor. The other is not seen or heard from again.
No mention of Mrs. Woodman is made despite the fact that she is still Lisa's mother regardless if the divorce mentioned earlier is a reality. No character mentions her: not Lisa, not MacGyver, not even the police.
The phone-trace machine displayed the caller's number, so it wouldn't matter if the caller hung up before the location was displayed; since the agents had the number, they could still find out where the phone was just by checking the local phone companies' line-installation records.
When the one kidnapper locks Lisa into the chamber on the parking deck he uses a padlock. Either he used the one that belongs there, but that means he would have had a key or he cracked it before the kidnap and it still locks, or he brought a new one to replaced the cracked one.
If there was no padlock before (which would be very unlikely since they were keeping things there) he also had to bring a lock.
Later the mall maintenance guy frees Lisa by opening the same padlock with his own key.
The ransom-bag was a million dollars short, yet Mr. Woodman tells the kidnapper that all the money is there.