I have been seing this problem for a very long time, so I don't know if this is winbox or routeros related.
I mostly saw this on virtualised systems, but that doesn't mean that it can't happen anywhere else .
The problem is that Winbox forgets about the network interfaces, both ethernet and tunnels like PPTP, SSTP, OVPN, L2TP .. and possibly others.
The interfaces on the other hand are clearly visible directly from the terminal.
When I look at firewall rules that depend on an interface through winbox, it shows unknown interface ... suggesting that the firewall rule might not work properly ... but yet again, looking through the terminal - everything is in place and operation looks normal.
Please see the attached screenshot. Sorry about the many blanks. I have sent supout.rif to support directly.