I know your having fun with it, but it's not that hard to interpret what they meant to write.
I believe the article is written accurately with respect to the items stolen, " several items including a semi-automatic rifle, a magazine and jacket with official FBI markings stolen from an agent’s car."
If you take that list of items to be accurate, which I believe it is, then the article reads, "The firearm was a Colt M-4 semi-automatic rifle with a magazine loaded with .45 caliber ammunition. The jacket was an official FBI raid jacket." Ok, obviously there is an error here. The report is not of an M-4 with a magazine, but a Colt M-4 along with a magazine for a .45 that was a separate item. Perhaps someone more familiar with a Colt M-4 would have made the statement more clear, but grammatically speaking, the only thing missing is a comma. It could have been written accurately as, "The firearm was a Colt M-4 semi-automatic rifle, with a magazine loaded with .45 caliber ammunition. The jacket was an official FBI raid jacket." It would have been better to make it even more clear the magazine was not related to M-4, but then we wouldn't have anything to laugh about.
On the other hand, the M-4 could have a .450 Bushmaster or .458 SOCOM upper and then it very well could have been the M-4's magazine that was loaded with .45 caliber ammunition, but I do not think the magazine would have been listed as a separate item unless it was indeed not related to the rifle.