There are several instances in this movie where Deadpool takes enough damage to appear to kill him and even sort of crosses over. However, since he regenerates naturally from each of these specific instances, they are not counted as kills.
4:13 Deadpool beheads a goon
4:16 He stabs a guy through the throat
4:19 He shoots a guy
4:27 He shoots a guy in the mouth
4:30 He slashes a goon’s face
4:32 He shoots another in the head
4:35 And then another
4:38 He stabs a guy through the chest
4:44 He stabs a guy through the head
4:52 Deadpool shoots 3 guys at a funeral
4:56 Then he shoots their boss in the head
5:16 He slashes a guy at a strip club
5:19 He causes one goon to shoot another
5:38 In this scene in Osaka, Deadpool stabs and slashes through 11 goons ending at the 7 minute mark
7:01 He takes out nine more in this section lasting through 7:39
7:45 Deadpool shoots a guy in the head
14:52 Goon shoots self with shotgun ricochet off of frying pan
15:02 Deadpool stabs a guy
15:07 Then another
15:10 He throws a knife to kill a thug
15:41 Vanessa is shot
17:39 Deadpool causes the guy that shot her to be run over by an ambulence
43:54 Deadpool shoots the orderly he says looks like “Jared Kushner”
52:27 Cable explodes a wall into a prison killing 2 guards
52:55 Cable causes explosion that kills 3 more
53:33 Cable shoots a guard 3 times
53:41 Then he shoots another in the head
55:43 Then he shoots another
1:13:07 Bedlam is hit by a bus
1:13:25 Shatterstar is splatter by helicopter blades
1:13:38 Vanisher is electrocuted
1:14:04 Zeitgeist is killed by a woodchipper
1:14:23 Technically I guess he dies here as he spits acid killing Peter
1:15:49 Explosion at a gas station gets the driver that was run into it as well as a parked car that is propelled towards the screen
1:16:18 A Driver is kicked out of a convoy truck by Domino
1:16:45 An explosion takes out a convoy car
1:17:26 A mutant expelled from the convoy is hit by a car
1:18:27 Deadpool shoots a guard
1:18:49 Several vehicles are squished by an out of control convoy truck killing at least a driver. Some seemed like they might of gotten out without damage, but the drivers of the taxi, the van, the red car and the SUV would have died.
1:19:35 Black Tom is shot by Cable
1:42:24 Cable shoots an orderly
1:42:37 Domino stabs one in the eye
1:42:39 Cable shoots 2
1:43:07 Guy slips and breaks neck on bed frame
1:43:10 Guy slips and stabs self
1:43:26 Lockers behead an orderly
1:43:42 Cable shoots one and then another after a cut
1:43:44 Cable shoots the guy holding Deadpool and then another guy dies off screen
1:43:53 Both Cable and Deadpool shoot a guy simultaneously
1:54:44 Deadpool dies from gunshot
2:01:16 Headmaster is hit by taxi
2:05:17 Deadpool kills the goon he killed earlier with a cheese spreader
2:06:16 Deadpool shoots the terrible version of himself from Wolverine: Origins
2:06:51 Deadpool shoots Ryan Reynolds after reading the Green Lantern script
Total: 88