It was not really a "mystery". Prowl had comprelling reason to believe that Spike had deviated from the terms of the Autobot/Skywatch deal. Part of that was "no killing Transformers". This ties in with "For all Mankind" and the Prowl "Spotlight" issue (which was meant to be told in flashbacks in the main book until the fandom's whining compelled IDW to publish it on its own). The story was Prowl trying to play by the rules and no accuse an ally of mischief. Prowl gathered evidence for diplomatic and moral reasons. (Prowl more or less knew, but he wanted to have physical evidence.)
These are honest questions, since I never read Police Action:
*sigh*
But, the wiki says it is bad, right?
What clues were there, that Spike was buying weapons from anyone?
It was stated in the "Spotlight" issue and (I think) "For all Mankind" that Spike's unit was using technology derived from Cybertronian tech. (The exo-suits and other armaments were not human designed/engineered.) "For all Mankind" specifically characterizes Swindle as being and opportunist. And, a huge theme in Costa's run was that TFs and humans can (and will) do business for mutual benefit despite a mutual lack of trust.
Swindle was not really the bad guy. He had nothing to do with Scrapper's death beyond knowing the guy who did it.
And, the evidence from Swindle was arguably circumstantial.
The only real problem with "Police Action" is that Spike used common Earth chemicals (commerically available stuff that anybody could get) to take out Scrapper. (Seriously, it raised the question of why humans would need to buy tech from Swindle or hire Cybertronian mercenaries in the first place.) But, Swindle's testimony (for lack of a better term) implicate Spike enough to justify Prowl confronting him with his (very grounded) suspicions.
What groundwork was laid to suggest that he was buying those weapons from Swindle specifically?
Again, I will restate
the story was not a mystery. It was just about Prowl trying to play by the rules (as a result of his new idealism after the events shown in the "Spotlight". (The "Spotlight" kind of clubs the reader with that point. But, given how dense the fandom can be, I will forgive Costa for that much.)
In any case, when Prowl is investigating Spike, he runs across Swindle.
Could any other Transformer have stood in Swindle's place without affecting the story?
Yeah sure. But, ultimately, chawuctuhs are fungible.
Did any of the bots ever question where SkyWatch got their technology prior to Police Action?
Did any of the humans ever question it?
Prowl and Streetwise were displeased that humans were using Cybertronian tech. But, they were more worried about how it was being used more than how people got ahold of it.
Humans were just happy to have a way to kill aliens. (And, really, why would they not be happy under those circumstances?)
One of Spike's subordinates characterizes him as a being a thug who was well connected and just good enough at his job to enjoy and exploit his station without repercussion. I forget the phrasing Costa used. But, Spike was essentially a highly competent warrior, but not a professional soldier. This made him completely unfit for command.
This idea is clearly there in the first issue, when Spike uses Breakdown as his ride. Taking trophies and other goodies is unbecoming of a leader. It is expected of a grunt. But, even they are not supposed to be to ostentatious about it. Spike would theoretically be allowed to annex facilities and similar infrastructure. But, a car? (Remember, Spike was not really seeing TFs as individuals at that point. And, even if he was, a modern commander would not be allowed to take captured slaves.)
Costa's run relied on people being interested in ideas and having frames of reference beyond "big wobuts is awshum". And, that got him in trouble with the people do want "comics with Transformers" more than "comics".
And, yeah, Costa was right to shit on the fandom towards the end.
Dom
-recommends Costa's run on "Cobra", DC's "Blackhawks" and IDW's "Smoke and Mirrors".