You specified the shapes incorrectly. You wanted a single shape consisting of 2 arcs and 2 lines, forming a single, simple, closed shape defining the hole. Instead, you sent a whole mess of self-intersecting shapes such that no human or machine can unambiguously figure out which parts of the board should be present or not.
Specify your edge layer such that EVERY line and arc actually delineates a border between PCB and air (unlike, for example, the horizontal lines in your picture which delineate absolutely nothing, they are supposed to have air on either side of them), and such that every line/arc is connected to precisely one other line (unlike, for example, the points at the end of your horizontal lines which have FOUR lines/arcs intersecting at a point, what the hell is that supposed to mean?) and you'll have no problems.
I mean, I bet you were thinking while you were drawing this at the design stage, "I assume they'll get what I mean by this, right? Right?". Well, now you've learned an important lesson for delivering engineering design artifacts -- never leave any scope for misinterpretation.