You definitely need to watch their categorizations closely, or it will spit out garbage. For instance, move $500 from checking to savings? It picks up the sending and receiving side of that separately, and counts it as a $500 expenditure, and $500 of income, which is just crazy.
Their auto-categorization is also overly aggressive sometimes. Say you deposit a check at an ATM, and then recategorize it as "Gift from Mom". Next time you deposit at that ATM, it will most likely auto-categorize it as the same thing. This also happens when you pay the same company for different things (eg, multiple kinds of insurance through the same company).
I mostly used it for tracking rather than budgeting, and I eventually decided that I prefer doing my own analysis. So I use Mint to aggregate transactions and categorize them, then use the "Export" to dump them all into an Excel sheet that analyzes things the way I want them. Works better for me, by YMMV.