the glitch makes the game "shake" varying in severity, it's usually the bees flashing out of existence and then coming back but some times the map would also "shake" and "flash"
Hmm, definitely haven't heard of anything like that before. You're saying it only happens when storage is full, and stops once you use some resources or construct more storage? If the game is running slowly, does this still happen if you disable shadows and particles, and turn antialiasing off in the Video Settings menu?
I'd definitely be keen to see a log file and some system specs (in particular CPU, RAM, graphics chipset, and VRAM, but a model number should be enough for me to look that up if you're on Apple hardware). If you're able to get a short video, that would be helpful too. Best to send those through via email, since the log contains your home folder path when outputting where it saves games to.
It's not that I don't believe you, it's just that I can't reproduce this and don't have enough information to guess at what might be happening, which leave me with no ability to even attempt to address the problem.
If the issue doesn't show up in images captured via the in-game screenshot key (P), then that would be useful to confirm.
The main thing I've been asking for though, has been your save file and a copy of the game log from a play session where the problem has occurred. Are you planning to send those through?