In terms of continuity, the Blackfyre Rebellions period got messed around with a bunch. Initially, Aegon V fought the War of Ninepenny Kings, now Jaehaerys II was King. Initially, Maekar I threw Bloodraven into the Black Cells – now Bloodraven was Maekar’s Hand despite the two of them having had near-civil war levels of dislike and mistrust in Mystery Knight, and Aegon V was the one who threw him in the cells prior to sending him to the Wall.
WOIAF also threw in some big problems with continuity – in addition to textual errors like Baelor coming before Daeron on the list of kings on the very last page, you also have things like Theon “the Hungry Wolf” Stark being King in the North during the Andal invasion and fighting Harrag Hoare on p. 138, and then Harrag being described in the Iron Islands section as having lived hundreds of years later. You can find some threads here and here.
In terms of timeline stuff, right now I’m having real issues with Cregan Stark and his kids and their kids all fitting in between 157 and 212. Also, given the sheer distances involved, it’s really improbable that almost all the wars in Westeros’ history were a year or two long. You’d expect some longer conflicts at some point.
Mostly, I’ve noticed cases where GRRM changes travel times to make story moments work. For example, Tyrion warping to the Inn at the Crossroads to meet Catelyn, which just does not work.
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