"What are you up to?" is a phrase whose implications vary with the context. Asked by a friend in casual converation it is just a pleasent enquiry about what you've been doing recently. Asked by a policeman when you are lurking in an alleyway with a crowbar, and it has a rather different connotation, and strongly implies that you are doing something wrong.
In the context quoted in the question, it does have a rather accusatory tone. It sounds something like "what are you fools playing at?" or "what on earth are you doing?" - it carries the implication that you assume the other person is doing something stupid.
And since the other person is your manager, they are even less likely to take that well.
That said, your manager talking about raising it to HR seems like a big overreaction, rather than just talking to you about what you meant and sorting out any misunderstanding (since email is notoriously lacking in tone and therefore prone to have the tone misread - written phrases in email tend to sound harsher and more judgemental than if you said the same thing in person).
Your best bet is probably to apologise for the phrasing and explain that it was meant more as an enquiry than an accusation.
For the future, something like "Is there some kind of problem at your end?" or "do we know why there is a sudden increase in escalations?" rather than "what are you up to?" would probably be a better way of phrasing it.