I got off a 50€ autostrada penalty after driving through a toll gate without collecting a ticket in Italy last year. When I couldn’t get through the barrier at my destination, an attendant issued me with a ticket for the maximum fare, due for payment within 15 days.
Luckily when I searched the autostrada website I found that the penalty could be challenged if I could provide suitable evidence (what they deem suitable evidence, I’m not sure – this page wasn’t available in English, but my hosts translated it for me). I photocopied my flight confirmation and car hire agreement, which showed where I’d arrived (Pescara airport) and approximately when. This was proof that I could only have entered the system at one point and hadn’t been driving around the autostrada all day. As the local toll station was closed until after my departure, my hosts later presented these documents and the ticket at the station when it reopened.
There ought to be a simple way to challenge similar penalties on the bike hire scheme, although in this case they might argue that you could have loaned the bike to someone else who returned it for you on Monday morning. I can’t see them going to the bother of checking cctv footage, even if they could access it. Fingers crossed someone there is willing to give you a break!