Hi Caleb and welcome to the Do-It forums.
The mold does have an odd configuration. Are you injecting the long side after injecting the short side? If you are, try reversing your injection order to see if bubbles still are an issue. Most bubbles in a bait are do to air in the plastic inside the injector. Are you purging [depressing the injector rod to get a small amount of plastic out of the nozzle while holding the injector with the nozzle straight up] the injector after filling it? Are you pouring the plastic into the injector with the nozzle removed or are you pulling plastic up thru the nozzle directly from a cup? Lots of variables here that can allow air inside the injector.