I doubt that having "too many objects in one cell" is a problem as I have have made huge structures with hundreds of objects. The geck can be quite frustrating at times, so here are a couple of things I like to do.
After I have built my structure and checked it, I like to leave the "snap to grid" on while I am cluttering an area. Once I have gotten all my clutter near the final location(s), I come back and turn off snap-to-grid for precise placement. Many times while I am selecting and moving multiple objects I have accidently added a piece(s) of the structure and moved them without realizing it. It's much easier to catch when the snap-to-grid is on. I also try to not zoom in too close when I am working as it is easier to spot an accidental selection.
I also like to keep an eye on my cell view when I am selecting things because sometimes it may take several "clicks" on an item to select it, but you also might be selecting something else by mistake and not realize it. I'm not sure if this is how you ended up with the gaps....just a couple of tips/thoughts.