Go with the meeting presentation/inquiry option. Note the overage and ask for explanation in a general question to the group - do not pose the question to the President. If the Pres speaks up about the decisions made you can directly inquire as to why others were not consulted ... try to find out if the decision was just & the circumstances.
Also check the bylaws. Is there anything in there about 'acting as one' PTO? Sounds like the Pres is going over heads (acting in the best interest but seems to have forgotten the team aspect) and not informing others of her decisions ... most decisions should be done as a body unless there is just cause.
A polite professional reminder in the form of Q and A at a meeting should help.

Stuff like this has been going on for quite sometime, we decide something and she does what she wants. There is alot that everyone have been swallowing and my phone rings all the time, other members complaining about her not doing what we have already decided on, or even better we decide for someone to do something for example prizes for this carnival, we tell them what and how much and they are suppose to do it and come to find out the president went out and purchased some prizes for the carnival and so the amount has gone over the amount alloted because the person in charge has already purchased all the toys...I need to bring this up but don't know the best way to approach this

Well--of course check the bylaws and see if there are any provisions for overages...if not...then it depends on how much of a fuss you want to make. You could demand the President make restitution (for as much as that will get you unless you are really ready to go to court over this)and OBTW that kills your relationship, you can swallow and remain graceful so the school thinks it was all part of the plan, or you can hold an after event meeting and make the budget a specific target of a discussion. Without being confrontational, you could bring up the fact that the concessions went way over budget and that next year you'll need to figure out a better way to stay on course so that everyone is comfortable with the cost of the event. No need to point fingers at the Prez...since you all know she did it..and then implement whatever procedures you come up with for the very next event. Maybe joint shopping, or "here's 200 dollars cash...anything over is a donation" or We have a 200 dollar cash card that the Treasurer has bought for this event to facilitate your ease of shopping--of course donations are welcomed if you choose to spend over that. OR maybe emergency approval provisions. In our group, the President authority to authorize 80 dollars in spending (not cumulative) each month. That solves the problem of chasing down everyone in the event of an overage.
I would go with 3 especially if the carnival was fun, and everyone seems to think the Pres did this with a positive spirit and not to be deceptive. Even President's make mistakes...I recently committed "us" to a fund raiser for adopt a classroom that will have 800 dollars in up front costs. I made a mistake, told the board that I had made a mistake and offered to bear the brunt of the up front costs myself if they disagreed with the fundraiser. They all supported the fundraiser but I sure felt better that I requested a mea culpa for saying "go" on the event without discussion with some of them.

Most of this is up to you and the folks in your group...
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We recently had a carnival, actually just Friday and prior to all this we of course had a meeting decided how much we would spend on what, well here's the question... We allotted so much money for the concession stand and the president has gone way over that amount. Prior to our last meeting we went to the store and priced how much everything for the concession would cost approx 200.00 (we are small), so that is what we apporved her to spend, well to find out she has purchased the chips alone for 180.00 which is ridiculous.. After the carnival a 2nd grade teacher walked up to me a thank me for the pop the PTO donated for her pop walk, that too wasn't approved either. So what should happen now