Welcome to TFF.
First off, there should always be a substrate in an aquarium with fish. The substrate--not the filter--is the primary bacteria bed, and there are many species beside nitrifying involved, and they need a home to maintain a healthy tank. For various reasons, some of these bacteria cannot colonize and function anywhere but in the substrate.
Cleaning a bare bottom tank involves daily vacuuming of the detritus; normally this would fall into the substrate, and various bacteria would break it down. This takes considerably longer with a substrate to house this bacteria, and this is part of the problem. Bacterial and other issues can easily occur in such an environment, which is, frankly, dirty. Second, you should clean the bottom glass with a sponge on a regular basis; I've no idea how often this needs doing, just that it does, same reason as above.
More frequent water changes are also needed with no substrate, again because you are leaving out the most important biological component of an aquarium and that has consequences for the fish.