The way he pulls his foot back registers more than the bump itself; she's accustomed to the physicality of his comfort, his habits of touching her. It's not exactly that Mulder has no concept of personal space; it's just that he considers it communal property.

But the question he asks is far more noteworthy. Does Skinner know, which means he doesn't know. That's a sobering, shattering thought. That Mulder might not know how to reach Scully. (In any time, any place-- how could he not know?)

"He wasn't able to get in touch with her." Which could mean anything, but probably means there's only one Dana Scully in any given moment. Honestly, part of her is relieved that she isn't going to have to face herself; it sounds even more alarming than this is.

"You think we switched places? Why? How?"