My thought exactly 
I would also ask in a non confrontation way, just like @temba and @Silversitters said, while adding a note that the unexpected difference might miff other sitters.
The key opened the front door, so I think so! 
The real reason I’m sure is the wet cat food is exactly where he said it would be.
I can do this, but do I ask ASAP or wait for the end of the sit like @Maggie8K said?
Being honest here: If it were me I’d probably have called as soon as I walked in and saw things looked different because I’d be terrified that even though the key worked, address etc, that I’d somehow walked into the wrong place and soon the real homeowner would walk in and boy would they be mad! 
Seriously, I don’t think I’d wait. It is disorienting and if you don’t sound critical, just curious, you can bring it up. Just don’t make it sound like an accusation.
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Edit:
You can tell I haven’t had coffee. I meant to write that I would do it while on the sit.
After all, inquiring in a friendly way as to what is going is very normal, since you did observe that the place was different before.
I bet that the house owner is wondering when you’re going to bring it up.
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