Yes, they certainly will, and if you leave them for long enough the chunks will get moldy!!!!!!!! I find it's generally true that if you leave the wafers in for longer than a day or so, the fish lose interest (kinda like my cat and her kibbles). I'd recommend using half a wafer if the wafers you're giving are consistently not being finished. If there is any left after the day, fish that out. It will only foul up your tank and make your gravel vaccing harder (if you gravel vac).
Also, how many algae eaters do you have in what size of a tank? You may not need to give them the wafers all that often.
Jonathan