User blog comment:Garhdo/Plot hole?/@comment-1221773-20111225154639/@comment-217683-20111225224910

I'm with Commdor on this one. In order to retrieve Shepard's body, they first would have had to be able to locate it. A sole body floating in space with (as far as we know) no means of location other than visual sighting. Then, assuming they could locate it, they would have needed to bring it aboard and, as Commdor points out, there's no indication they have the tech to do so. And yes, they were likely concerned about detection as well. If a Spectre's ship, not to mention one of the most advanced ships in the Alliance, is attacked, you can expect a heavy response. The Collectors didn't want to attract too much attention, so it was a hit-and-run.

As for why they later went after Shepard's body once it had been located, that answer is simple. Because it had been located. The hard work had already been done, they saw the potential to use it and, most importantly, they wanted to deny their potential adversaries (Cerberus, the Alliance, etc) of Commander Shepard. We saw why they would want to do so in ME2. It's not a plot hole. It makes perfect sense and is, in fact, integral to the plot.