It’s really not that hard to tell whether a romance book is supposed to be in an SF category, in most cases. Taken by the Alien Alpha Barbarian is not Military SF just because it’s set in space and the barbarian beats up a few people.
If the romance is central to the story, and the spaceships just a backdrop, it’s a romance, If the romance is a subplot and the spaceships are the focus, it’s sci-fi. I’m not sure why this is hard to understand. Just think about which part of the book you can remove without destroying the story, and it should be pretty clear which category it should be listed in.
Yes, there’s a grey area where you’re exploring romance in a radically different sci-fi world. But those stories are a) relatively rare, and b) probably sci-fi.
No-one’s complaining that there are girl cooties in SF novels (well, OK, a few nuts might be). They are complaining that they go to the SF bestseller list and find that 50% of them are romance novels in spacesuits. I stopped bothering to check the list a year or two back, because it was so stuffed with romance books that there was no point any more.
And, as others have said, a large part of the problem is that Amazon use the keywords to pick categories, rather than just letting authors do so. If you put ‘space barbarian’ in the keywords for your romance novel, it will probably end up somewhere in SF. If you put ‘romance’ in the keywords for your Military SF novel because there’s a romance subplot, it will probably end up somewhere in romance.