I am having a problem with a certain instance. When I load up the instances/gameplay/cube_dropper_normal.vmf
instance, it does not work. Instead, even though I have a Logic_auto connected to it to enable the auto respawn, it fills with cubes. I tried searching but found nothing of the sort. I do in fact think that I am doing something wrong. As it could not be the instance files, because I have verify'd them. Thank you in advance.

do you have multiple cube_dropper_normal's in your map?

It's a known bug. You can always try downloading a custom instance pack or dropper in the downloads section:

They be brilliant and would use over Valve's anyday! (I use ones Skotty made, not sure if he released though)