It's probably more subtle than that:
As part of the dispute, Croatia didn't claim it, and neither did Serbia.
But in the meanwhile, Serbia did control various other disputed areas. So it would make sense that in turn, Croatia did the same with 'Liberland'. There's no contradiction between [not claiming an area] but still [asserting some degree of control there].
'Liberland' people claimed homes demolished "without warning" etc, but then complain about having been harassed for years.
So, more likely there were previous warnings, legal procedings or whatever, Liberland ignored those because 'not in our country, doesn't apply', and at some point time is up.
Given its history, it's logical Croatia would be sensitive about border disputes. And then some 3rd party steps in, complicates things & proclaims a new country between your neighbour & yourself?
Can't have that! So this whole clearing operation would simply be "what a nuissance these people! Let's fix that" on Croatia's side. And in the process, assert some control over the area.
All in all it seems the Liberland folks are rather naive about land being abandoned, or how border disputes work. Possibly no-one would care if they'd just squatted there without proclaiming anything.