Hi Bazinga,
It’s not clear to me that the cover has an issue or a defect from your pictures but it can be a little more tricky to work with a putting a stretch cover around a latex mattress when you are dealing with a complete mattress that has layers that are glued together instead of individual layers (individual layers are a little tricky as well to place them in the cover squarely so they are even and laying flat).
I would probably suggest that you put the cover inside out around your foundation first (see the video here from about the 3.00 minute mark) so that you have a square surface on the bottom that fits squarely around the foundation and then very carefully (you will need two people) put the mattress on top of the flat bottom of the cover and then make adjustments so that the mattress is square with the bottom of the cover all the way around. Then you should be able to pull the cover back the right way again to fully enclose the mattress and then if the cover is the right thickness you will be able to carefully zip it up by compressing the latex slightly where you are zipping (the latex will usually be a little higher than the cover so that the fit is tight). The sides should go faster but you will need to go carefully around the corners.
I would also talk with them on the phone rather than emailing them (see post #4 here) so they can provide you with any other suggestions that may be helpful and if you believe your cover has a defect I would send pictures to Mattresses.net that clearly show any defects before you call them.
Phoenix