As I understand it, a decent amount of Scottish funding and budgets are based largely on a proportion of spending in England, so if the English MP's vote to cut NHS funding for example, the proportion of NHS funding going to Scotland would also decrease, and Scottish MP's wouldn't have had any say on it and MSP's wouldn't have any way to counter it within their budget setting powers.
Proper devolution / federalism would have devolved all of these budget setting powers to Scotland (in fact, I thought that's what the vow was all about), but that hasn't happened yet. So if I've understood it properly, you can see why the Scots think they're being screwed over. They've not got the powers they were promised, and they won't be able to vote on issues that do affect them.
But I might be wrong!