This isn't like the standard "Will they/won't they" deal, at the start of the season they had that talk where without actually saying it they admitted to having feelings for each other, and there have been so many scenes throughout the season that have showcased this; such has how Beckett was when she found Castle still alive in the bank raid, to the scene a couple of eps ago where she put her hand on his when Martha was doing her play.
Castle is a case of "When will they?" and has been all season, hell he even told his mother how he feels about Beckett so it's not in the usual doubt territory adopted by the premise.
In the convo they had at the start of the season Beckett in as many words asked Castle to wait for her to get her self together and lower her wall, and he accepted that, however something had to act as a catalyst to move us on and this crossed wires situation is great because it is going to take the story where it needs to go and we get to see Castle act like a prat in his hurt state, before they have the scene together where they lay it all on the table.......only to semi fall out again once she finds out he's lied to her about her mothers death and return to being friends until she feels she can truly trust him again.