Hello,
I'm not sure if this is a bug after all, and it is not important, but I just mention it. ;D
When I was fighting against the fourth boss, this kind of plant, I noticed that some of the little things it sends out were somehow flickering. I mean that they turned invisible and just appeared sometimes for a short time. Attacking or being attacked by this monsters works absolutely fine. Also, if you hit them with the hookshot, they become visible permanently. So probably it's meant to work that way, but I thought I might be able to help someone if I mentioned this...
-The bread
This looks like a bug indeed. I never had this problem.
If they're flickering energy balls it could be that they're flickering at a speed that your screen can't handle, which causes them to be drawn only on the solid frame or the transparent frame, not one on one off like it should be.
If your monitor supports higher refresh rates (60hz, 70hz, 80hz, etc) try one of those, and see if it persists... (Or look for the script that defines them and change the rate they flash)
If they flash at a seemingly random rate, its probably the refresh rate of the screen.
It could still be a bug though. (and probably should be a bug anyway if its not drawing correctly at all refresh rates anyway)
tl;dr
Could be a hardware issue that the script doesn't account for.