when Petyr and Jon had the confrontation in the crypt
Petyr was egging Jon on and at the moment he mentioned his love
for Sansa is when Jon lost it and choked him , when Petyr came out of the crypts
there was a close up of him looking at Jon and then Sansa looking waving
goodbye to Jon as he left
I think Petyr was suspicious or realized that Something may be going on
between Jon or Sansa or most realized jons feelings for Sansa
another hint Petyr mentions "gossip" about how beautiful the dragon queen
Is to Sansa and how Jon may want to marry her , why would he do that ?
Petyr wanted to get a reaction out of Sansa
she said what does her beauty has anything to do with that
Petyr was a smart man and could see things and play with people's emotions
I think he knew that Jon and Sansa may have romantic feelings between them
he knew and brought up to both love and marriage and in a way already set up
a triangle between Jon Dany and Sansa