Speaking from personal experience, ignore such warning signs at your peril. I wrote about what happened to me a while back, and there are enough similarities here that you might be interested in giving the story a read [1].
If you choose to fight over this issue, it's going to come down to the attorneys. You'll have to decide early on what the desired outcome is: do you want out, presumably compensated for your earlier investment, or do you still want to be part of the company with the rights due a shareholder? If, as I assume based on your wording, you invested money into the company as well as your labor, that helps make things much more clear cut which would make an agreement more likely. It'd still be long and messy, but not as long as a fight without that investment. It's also possible that just hiring counsel will help them budge. Legally, there's no real reason for them to delay awarding equity for three months unless they're purposely trying to prevent you from exercising any input during the incubator program (and with any negotiations that occur during that time). At a very minimum, it makes things more difficult for them by hampering your relationship--and that's something any outside investor will eventually stumble upon and start asking undesirable questions about assuming it doesn't scare them off entirely to begin with.
That said, even if you prevail without having to litigate, you're still going to lose. That, unfortunately, is inevitable: your co-founders have already amply demonstrated a willingness to stick a knife in your back. Even though shareholders have certain rights available to them, there's no guarantee your co-founders will bother recognizing those rights. There are a myriad of different ways in which a minority shareholder can be oppressed and frozen out of the business. Whether they're making decisions without informing you, cutting your wages outright (it's not like they'll be paying dividends for some time), or purposely diluting your shares, they have the ability to make your life miserable with a fig leaf of justification thanks to their majority status and your only option for recompense is through the courts. And while it's likely that you'd eventually succeed, it'd only be after lengthy and expensive litigation--assuming, of course, that the startup doesn't fail by the time you're done (and the battle itself would certainly harm the company, particularly in the eyes of potential investors).
Leaving hurts. Being forced to leave hurts even more. But sticking around? Even if you feel that you win this round, even if they capitulate immediately, the knowledge that countless more are waiting just around the corner will wear you down. It'll wear you down, suck away your savings to pay for constant legal advice even if you manage to avoid litigation, and it'll do so while destroying every last thing that made you want to found a startup in the first place. One day, you'll wake up and wonder just what happened to you thanks to what was, in the end, nothing more than a pyrrhic victory.
You won't be the first, and you most certainly won't be the last. As it stands, you're in a no-win situation. Consult with an attorney before you make a move to avoid any potential problems (for instance, how much code did you write yourself versus other programmers/employees), take your code, and walk away.
P.S. - If they're planning to get rid of you once all "the code" is written, it's unlikely that the startup is going to succeed in the end anyhow. That sort of short-sighted attitude makes it abundantly clear that your partners have no real desire to improve upon the product over time.
[1] https://news.ycombinator.com/item?id=7579845