Were there, historically, any repercussions or limits to how and when a lord could choose to disinherit one or more of his heirs? Robb could cite the fact that Sansa is a woman forcefully married into the family of his mortal enemies and Tywin could point out that Tyrion is a dwarf (and thus cursed by the gods) but could any heir be disinherited at any time by their liege?

There could be – civil wars have definitely been started over disinheritances or disputed successions. On the other hand, there are plenty of cases where that didn’t happen – Alfred the Great, for example, succeeded his brother despite his brother having adult sons, but Alfred had more support among the nobility of Wessex so managed to tough it out. 

It really depends on the political circumstances.