I'm not sure whether this only Iron clan, but we have a problem with the Chakra Flow in our skill tree. This was brought to my attention by another Iron.
How do I explain it? The closest I can think of is our chakra isn't affected by Chakra Flow if we invest in it before reaching our desired intelligence stat. So you're spending more chakra than what you're regenerating.
Here's a workaround for the bug until its fixed/looked at:
Invest one less than your desired number in Chakra Flow, then gain all the intelligence you want, then invest that last point in Chakra Flow. If you want more intelligence you have to do the whole thing over.