This is a known problem with some of the commercially sold plastic racks. I don't know of a permanant solution that is convenient to eliminate the upper shelf from sagging down and rubbing on the lower box.
This solution is not convenient but it will work.
Cut a piece of 1/4 or 3/8 thick plywood, pine, or melamine to the same size as each shelf hole. To check for fit, insert your box and then the wood. The fit, top to bottom should be snug enough to hold itself in place and keep the shelf level. At this point you cannot see your box so you need to cut the center area out. Leave a 3/4 - 1 inch area around the sides and cut out the center. You now have what looks similar to a picture frame. Insert one into each hole/shelf. Make each one per shelf and mark them because your shelves are not likely to be the exact same size. This is not a pretty solution but it beats the hell out of fighting with boxes and spilling water bowls every time you pull out a box.
The thin plastic racks that I bought the first time had this same problem. They held a 32 qt box sideways or 2 15qt boxes lengthwise. I made shelf dividers the same height as each hole/shelf. They were long enough to run the full depth, all the way from front to back. I made 3 and placed each into the shelves. When viewed from the front it looked like one tall divider. They were placed right on top of each other supporting the same spot on each shelf. This eliminted the problem for the racks that used the smaller boxes.
Just a note about the possibility that a snake may get out. The shelves sag in the middle. On the ends there is very little sag. If your gap on the end is so big that a snake may get out, it is too big of a gap to begin with. The supports mentioned above will only help with the sag, rubbing of boxes, etc. If that gap is too big to begin with for the species you keep, place something under the box to raise it. Newspaper, 1/8 or 3/16 peg board, press board, etc.
