Yes @Lis33 , I also had a bit of a query whether she was wearing your t shirt or something.... lol.
As others like @Anonymous , @Wendy117 , @Rachel177 have stated, this is quite a tradition in Asian countries.
Do buy a couple of pairs of cheap thongs (flip flops for you foreigners) and leave them in a common area as previously mentioned, and wash after guests leave.
But, if your thongs were not left in a common space, but a personal space, as @Helen3 has said, you need to emphasise the room and area boundaries, which may need to include a lock.
In Darwin, we tend to take our footwear off when entering the house, I have thongs near the front door and another pair on the back balcony, for a quick run downstairs. Maybe it’s because of the heat and traditionally having jarrah floor boards or tiles, or maybe because we are the Asian gateway; but I usually wear thongs when doing a check in and also flick mine off when I enter the clean homestay space. I just say, it’s their cleaned space if they query my actions.
I carry thongs when I travel, and even my dentist in Hanoi requires you to take off your footwear and use the slippers (plastic slide ons) provided.