$AnchorScroll is instantiated when ngInclude is compiled. Instantiation sets $AnchorScroll's watcher and calls the listener, scrolling the window to the top:
https://github.com/angular/angular.js/blob/master/src/ng/anchorScroll.js#L96

It seems that checking for $location.hash inequality in autoScrollWatchAction() before calling scroll() would fix this issue, though I'm not familiar enough with $AnchorScroll to know if that would have wider implications.

I understand that, technically, the instantiation of $AnchorScroll is unrelated to ngIncude's autoscroll attribute, but it certainly seems counterintuitive that this current behavior exists.

Example Plunkr:
http://plnkr.co/edit/XMuTqFmvKB7LzRyuzLSs?p=preview