Holding costs. They'll be more than you think when you first start out. Utilities, taxes, insurance, etc. Utilities will likely run a little higher than you expect because the property is essentially an active work site for at least 8-10 hours a day, for 4-8 weeks straight or more. If you're financing the project in any way (traditional loan, hard money, etc) make sure you account for those holding coasts as well.
Misc extra rehab items that you didn't think about. For example, let's say you have a pretty basic cosmetic rehab project. No major mechanicals to worry about. So you budget for carpet, wood flooring, maybe some updated countertops, some paint, etc. But, what about changing all the outlet and switch covers so they don't look like crap compared to the freshly painted walls? What about that crappy 20 year old light fixture that now looks horribly out of place next to the new flooring and countertops? Trim board that needs replacing because you really couldn't tell how beat up it was until it was right next to fresh wood flooring?
Those are just a couple that come to mind off the top of my head. Having a really detailed rehab spreadsheet with all the possible items you could encounter in it will help with that. If you haven't already , grab J Scott's Book on Estimated Rehab Cost. He's got a great template to use when walking through homes and estimating rehab costs.