So I was making a Two Hearted Clone (an IPA). I boiled 1 oz centennial hops for 60 min, then 1/2 ounce for 15 min, then 1 oz for 10 min, then 1oz for 5 min for a total of 90 minutes. I was supposed to boil for a total of 60 minutes adding each set of hops with the specified amount of boil time left. How will this mistake affect my beer?
Further to the other responses your beer is also likely to be darker than expected due to the longer time for Maillard reaction.
Your OG will be higher than expected as you have boiled off a bit more wort than planned. This will... give you more alcohol, which is ok. :) Unfortunately this also means less beer going into the fermenter and less beer going into bottles/kegs. :( Due to boil off your beer will have more body.
You may have more caramel/toasty notes due to the prolonged boil.
Bitterness might be a bit bigger, as Danny mentioned, but the condensed malt and alcohol should balance that out.
It's worth noting too (since this is an IPA) that in addition to the added bitterness, you will also lose a small amount of hop aroma from your last three additions. Late-addition hops are meant to go in late enough to minimize loss of volatile aromatic hop oils which are very prone to disappear as they evaporate during the boil. Of course (as already noted) there is really no detriment to this at all, but if you wanted to try to make up for it you could consider adding a larger amount of dry hops than called for (maybe + 10-20%), if you have them on hand.
Don't worry, this is a relatively minor problem (and a common mistake for new brewers).
I do a 90 minute boil on every beer, and strongly believe there is science to back up doing a 90 over a 60 for all beers (not just those using high amounts of pils malt to drive off DMS).
However, I still do my 60m. bittering hop addition @ 60m. If your bittering hops were in the boil for longer than that you will get a higher level of IBUs in your finished beer. Only you can decide if that is a bad thing; it certainly won't make "bad beer" but it will be more bitter than the recipe called for, than you expected, or that the style allows for.
I always boil my IPA for 90 minutes and start the hop additions at the 60 minute mark. This will give you a bit of a toffee character to your beer because the sugars in the wort will caramelize a little more. For some recipes, like a Scotch Ale, I'll take some (a couple of quarts) of my first runnings and boil that while I'm sparging and add it near the end of the boil. It'll leave your friends scratching their heads wondering why it's so good.