I discovered Wave Jump through the Global Game Jam website. It's a neat solution to the theme of the challenge. Thank you for creating and sharing this!
While playing the game, I observed that the score could accumulate by 1 to 3 points for Player 1, while Player 2 only accumulated points one at a time.
There might be a secondary issue as well. For each player, 2 additional markers follow around the principal one. I noticed that I could not collide the cloned markers with the target zone (aka cyber portal).
Player 1 multiple scoring
The easiest way to reproduce this is to use the (W,A,S,D) keys to move your cursor above or below the target. Move vertically to intercept the target. Observe the difference in your score before and after.
Compare this with the behavior for Player 2, performing similar actions.
Player 1 tended to score 3 points fairly often.
Player 2 tended to score 1 point exclusively.
Secondary object non-collisions
To reproduce this, use the arrow keys on the keyboard to manipulate Player 2's objects.
You will need to traverse the game board a bit to separate the cloned objects which follow your principal player marker.
Try to get one or more objects below the wave, if your target is also below the wave most of the time.
Moving left to right as well as up and down, you can separate them.
Next, move in such a way to cause the following objects (which don't have the blue tracers) to intercept the target.
In my observation, these secondary objects will not register a collision with the target.
Perhaps these two topics are related.
I reviewed the source here on Github, but didn't notice any root cause.
Perhaps checking it out and running it as per your build instructions might help.
Tested in two web browsers by visiting the published game's website.
Firefox (Quantum) 64.0
Google Chrome Version 71.0.3578.98
both 64 bit.