Debt depends on the relationship of spending to income, with assets taken into consideration. In the case of House Waynwood, it seems to be the case that they have been living above their means in order to maintain the “manner to which [they] have become accustomed.” As Catelyn notes, the Waynwoods are known for ceremony – which requires a show of splendor to reflect the status of the house, regardless of whether you can afford it.
In the case of House Grafton, they backed the wrong side in Robert’s Rebellion and got their city sacked. And while Robert was known for being forgiving, as Lord of the Vale and Hand of the King, Jon Arryn would have extracted a hefty penalty for their disloyalty to him.