Well there are a couple of options. If you're comfortable with doing these sorts of things yourself, you can file a motion to quash the certificate of offence. (LOTS of paperwork!) Beyond that, there are a lot of scenarios that could happen.
If you show up unprepared... here's the bad news: With you present for trial, the Justice of the Peace could (theoretically) amend the ticket to the correct HTA section, which is 136 (1)(a) for Disobey Stop Sign, and the trial could then continue. Conversely, the Crown Prosecutor may just decide to withdraw the charge on the basis that the ticket is defective. If you present a reasonable argument, though, the Justice of the Peace may throw out the ticket regardless. A complete conflict between the section and offence description (speeding vs. stop sign) should be sufficient to make the JP toss it, but you never know.
Or, if you wanted to, you could not show up for trial. Seems like a rather dumb idea, but the Provincial Offences Act, which guides these sorts of proceedings, has its quirks. If you fail to appear, the JP would then be required to examine the ticket for any "fatal" errors (conflicting section and offence description should count as a fatal error) and should then quash it. Here's a big, long discussion along those lines...
http://www.ontariohighwaytrafficact.com/topic1598.html Not exactly the same situation, but I'd say the "default" procedure applies here. Off Camber initially asked the Crown Prosecutor if they would withdraw the charge; they said no, they'd just amend it, so he walked out of court. The Justice of the Peace erred and convicted him, so he appealed, and won. The error on his ticket was both the set fine and total payable amounts were incorrect. If the JP did enter a conviction, you'd have to appeal it, but should win on appeal.
Alternatively, you could consult a paralegal and see if they'd be willing to take it on. Anyone who is reasonably qualified should be able to get this one thrown out.
I guess it all depends on how much time/effort you want to put into fighting this... Hopefully this helps a bit...