Funds do not need to be 6-months old. This is a misunderstanding of IRCC's requirement for persons to provide a 6-month history of their accounts. The 6-month rule is only to provide IRCC with enough history to figure out if the funds you're claiming for settlement are encumbered in some way (e.g. you took out a loan to get the funds, which you're not allowed to do).
As long as you can provide evidence that all of the funds that you have at this time are yours, unencumbered, and are free and clear to be used for nothing but your settlement, then the 6-month history doesn't matter. Provide documentation to help IRCC understand why you only have a 3-month old account (If you've been working for a year or more, which is required for Express Entry, you would have been earning for at least a year, so that would automatically raise concerns as to why your account is only 3 months old - i.e. is there something you're trying to hide? But as long as you can show proper evidence of why the account is only 3-months old and that there's no sketchy reason behind it, you'll be fine).