I... can not wrap my head around a not- awesomely wonderful Fergus!

However, I think there are good reasons, if you use the end-game decisions of letting Loghain live and not placing Alistair on the throne (Couslands are royalists, and very loyal to the Calenhad line), I can see him disagreeing with her.

Add in letting Nathaniel live, and a good dispute because perhaps she won't tell him what happened to his family during the siege, and some survivor's guilt, that could work.

I'm going to stand over here and hug Fergus, because talking about this is weird! Ha!