You might be better to be asking GO for the refund, not Presto. Just walk into the Customer Service office at Union (whatever the office to the right and around the corner from the ticket counters is called). They should straighten it out in no time.It took 2 hours for GO to get to Erindale because the Gardiner Expressway was closed. Plus the bus was really crowded both ways, with a dozen standees each trip, so it took longer for boarding and letting people off. The 38 also arrived 8 minutes late as well (you can check the schedule and see). I already email Presto for refund. No way I can accept being penalized $1.90 because both the GO and MT buses took too long.
Not sure what Presto would do ... as their stuff seemed to work fine, and did as designed.
Now, what should happen, is that they should fine tune the criteria for co-fares, to be based on your more recent tap-off time off GO, rather than your initial tap-on time. It's easy to imagine that you can spend 2.5 hours on GO and waiting for a Mississauga Transit bus, even when things are working right!