Sometimes chunks can still maintain the liquid color after you removed them.
Logout and login to fix this, that's the only way.
This is a Minecraft bug I cannot fix.
If you place normal water (or if it's naturally generated) on the top or on the bottom of a custom liquid you will see it will have the custom liquid color.
This is a Minecraft bug I cannot fix.
Custom liquids are not totally colored sometimes, some parts still have vanilla water color.