There's a lot of obvious clashes, but they don't bother me unless they're painfully stupid (see: Deception and Evolution). The whole idea of humans living all throughout the galaxy with established businesses and organisations so early into their space faring existence is itself silly, and that was established in the first game.
I guess, despite loving the franchise, I don't take it anywhere near serious enough to be offended by a lot of the clashes, not unless they're the aforementioned really stupid stuff (Evolution's handling of the First Contact War was awful). Otherwise even with the occasional lore confusion and clash, I love nearly everything of what ME2 added to the universe.
Sometimes I think, and I'm not pointing a finger here, but sometimes I think people's dislike of BioWare's direction with ME2 manifests as hatred for everything in the plot, even the stuff that 'makes sense' and fits into the universe. I've heard some people, for example, complain about the Collectors being Protheans, as if it is a stupid, nonsensical twist that doesn't fit into the established canon, when it is in fact the exact opposite, and ties nicely into established lore from ME1.
But I bought and read the books/comics so clearly I'm insane.
