The alarm reset button is on the top in one scene and on the bottom in the next scene.

The bundle of money being counted by the bad guys is blank on one side

As Mac falls after being hit by the bad policeman, his eyes are red, the same as they are when he's drugged. Then in the next scene they are clear again. (scene is a cut from the later scene when Mac falls and is found by the girl)

At the beginning the two germans say "Colson is here personally for the pick up" refering to Pete Thornton.. Colson was the character Dana Elca played in the pilot episode.

I’d like to discuss an already picked nit please.

I can’t find where they call Pete Colson. I hear the blonde bad dude say with an accent “Thornton is here to make the pick up, personally” as they are sitting in the car. This is the first thing said after Macs voice over about spending ages at sea. Is this the bit this refers to?
If so, maybe its an accent thing? I was thinking I could have been fooled in to hearing Thornton because I had my subtitles up and it wrote Thornton but when I am not reading the words it still sounds like Thornton to me. Unless I have well and truely fooled myself by my first listen/read. Does anyone else hear Thornton?

Hmmm... that accent doesn't help things.

But I think you might be right rat... It does sound more like Thornton than Colton

Pete is shot in his left arm; however, later he is shown with his right arm in a sling,

um.... no!

Watch the scene again.

I can’t find where they call Pete Colson. I hear the blonde bad dude say with an accent “Thornton is here to make the pick up, personally” as they are sitting in the car. This is the first thing said after Macs voice over about spending ages at sea. Is this the bit this refers to?
If so, maybe its an accent thing? I was thinking I could have been fooled in to hearing Thornton because I had my subtitles up and it wrote Thornton but when I am not reading the words it still sounds like Thornton to me. Unless I have well and truely fooled myself by my first listen/read. Does anyone else hear Thornton?

Nope the 'German' guy definitly says Thornton.

when mac is making the slingshot out of the bed he stands the bed upright you can see there is nothing on the top right part of the door but in the next shot mac walks over to get the springs that are hanging down

Don't you think there are major time jumps in those six hours?

When Mac is drugged they begin counting. By the time they bring him up to that room forty-five minutes have passed. What could they have possibly talked about for forty-five minutes if Mac refused talking in the first place? The nice weather outside? The price of tomatoes?
I'd say try talking, he refuses, drug him, explain him the effects of the injection and send him up to the room to the think. So I'd say only five minutes max could've passed.

But forty-five minutes after the injection he was send up to that room. Must've been an interesting conversation than, don't you think?

Also after Mac send Lisa away to call Thornton he looks at his watch again with like one hour and seven minutes left. By the time he reaches the warehouse again almost another full hour passed. Was it really an whole hour walking from where he was to the warehouse?

And another thing I noticed when Mac is escaping the room. He takes off his belt for the electrical diversion. You see him taking off his belt and unscrewing the socket with the pin of the belt. When he tries to attach the belt from the faucet to the socket it's too short so he unscrews the draining pipe and attaches his belt from there.

We know that. Big deal. But my point is when he attaches his belt from the draining pipe, you can see his belt is sewn together so it would look like a tube for the water to run through. Now how did that happen? One moment he takes off his belt, the next it appears to be sewn together and looks like a tube. Or maybe he wore his belt as a tube in his pants? But that would be rather uncomfortable, don't you think?

When it zooms in on the window of the room where MacGyver is sleeping at Lisa's place, it shows a broken window pane. When MacGyver looks outside the window, it's in one piece.