Hello,

I did a few tests on Kakashi Clone, using a team of Neji, Kabuto and Hinata (all 20 chakra mysteries for round 1).
In two scenarios:
1) Lightning Armor + Bloodthirsty Calm Mind - I could manually click all mysteries, without any delays or issues. Used Main on both Move1 and Move4, to make sure it doesn't experience any delays with moving between rounds.
2) Lightning Sealing Slash (to use Chakra), on move 4. Chakra gain by lightning main, was again possible to be used, without any delays or issues.

If you experience your bug in another scenario, please let me know, will try to test it out :)

Have a nice day :)

I'm strongly convinced that it is an issue of lag, as mentioned before.
However, if you are able to create a video/gif, that would showcase this bug, it could help a lot in making sure this is the case.