This is due to the skill name being used as the HTML ID, which doesn't allow spaces. This prevents the CP from changing if you're modifying the skill but the CP does correct itself if you change another skill. e.g.
Add 50 points to Kinetic Weapons,
The JavaScript error appears in the console,
The CP available remains at 1000,
Add 50 points to Navigation,
The CP available changes to 900
This also happens with knowledge skills with a space for the same reason.
Skills with a space in the name (e.g. Kinetic Weapons) cause a JavaScript error with the following message:
Uncaught Error: Syntax error, unrecognized expression: [id=Kinetic Weapons]
This is due to the skill name being used as the HTML ID, which doesn't allow spaces. This prevents the CP from changing if you're modifying the skill but the CP does correct itself if you change another skill. e.g.
This also happens with knowledge skills with a space for the same reason.