The back of Murdoc's camo coat is on fire after his flame-thrower's fuel tanks are set ablaze, and so he rolls on the ground to extinguish the flames. Yet after he gets up again and lopes off down the road, his jacket is unburned.
When Murdoc stabs his knife into the "Mountaineer's Guide to Widowmaker Pass" in MacGyver's houseboat to pick it up, you can briefly see several additional knife-marks in the wooden tabletop beneath it, most likely from either rehearsals of the scene or previous out-takes (in which the brochure probably fell off the knife as Michael Des Barres was raising it up).
Murdoc is shown rolling around on the ground amidst two flaming piles and thick smoke, yet in the next shot of him still rolling on the ground, there is no smoke, and the two piles of flame are some distance from him.
Between the time Nikki pulls up, walks into the cabin, walks out and talks with MacGyver, there was not enough time to Murdoc to sneak in and set up the pictures, mine the road out with at least a dozen mines, disable all the locks in Nikki's truck and plant the timer, especially considering his truck was parked so far away that it took him a few minutes to run to it from the Nikki's truck.
Murdoc was outside the cabin when Mac was speaking in a low voice to Nikki about Murdoc's being dead, so he would not have been able to hear what Mac was saying; he would not have known to say, "Not quite, MacGyver" at the right moment.
Murdoc informs Nikki that some of her truck's spark plug wires are frayed, but if that were the case, it would not have caused the starter motor to jerk and bind as if the battery was low; the engine would still have been able to crank, even if it couldn't have started.
When we see Pete approaching the door with keys in hand then discovering the glass broken, he reaches in through the glass to open it. He should have opened it from the outside because he had keys (if it was locked), and by touching the inside knob, he would have contaminated any fingerprints. At this point, all he knew was there had been a break-in. He did not know who it was.
Every picture of the 'R.I.P. MacGyver' shows a picture of Jack and MacGyver. When Pete is in MacGyver's houseboat on the phone with Helen, the fireplace is seen and that same Jack and MacGyver picture is missing.
Around 38:10, When MacGyver is climbing back down the face that Mike fell off of at the beginning of the episode, you can see a 3rd rope in addition to the two red ropes. Presumably, this is the real safety rope for the actor, and the red ropes are just props.
MacGyver says it's impossible and that Murdoc is dead, yet in the last confrontation, when we saw Murdoc supposedly die, MacGyver was singing a different tune, saying there was plenty of time for him to get out and still be alive.
When Pete discovers that Murdoc broke into MacGyver's houseboat he phones the Phoenix Foundation and instructs them to call the "DSX," actually meaning "DXS".