Guest not responding after working in host enviroment

I run whonix on debian jessie with MATE. I don’t know why but my virtual machines ( both workstation and gateway ) usually stop responding after a longer period of time of working in other virtual machine / in host enviroment ( so e.g. when I do sth on gateway / in host enviroment, sometimes my whonix workstatiion stops responding ). Do you guys know why it happens? How can I fix it? Is it somehow tied to transfering RAM to swap partition?

Try using one of the two major DEs.

Well, I mean I use default KDE on guest machines but MATE on host. Anything else I could do more frendly for my hardware and HDD?

KDE is pretty friendly too. MATE is a second rate DE based on an obsolete toolkit.