I’m a relatively new user of GB, so I’m sure this problem is something I’ve done wrong - but I’m stumped on how to fix it. I’ve gone back to September 1st and entered every transaction in all of the accounts I’m tracking. All of my account balances are correct. All of my expenses have been coded to the proper envelopes.
On the last day of September, I allocated all of my unallocated funds (I think) to the various envelopes. I assume that means that my unallocated funds should’ve been “$0” as of 10/01, and my unallocated funds as of today should be $0 + whatever income I’ve recorded.
However, that isn’t what I have. I’m WAY off and I can’t figure out why. I realize this is going to be nearly impossible to answer without seeing my budget, so what I’m actually looking for is the proper way to re-do all of this so I can get things corrected.
The first question I have is whether you’ve done any more fills since your Sept. 30th reallocation. If not, then what you’ve said makes sense—the Unallocated should still be $0 plus any income you haven’t assigned to an envelope. If you HAVE done a fill from Unallocated (say, something scheduled for the 1st?) then your Unallocated will be additionally decreased by that amount.
Is your Unallocated in the positive (you have extra money to use) or negative (you’ve overfilled your envelopes)? And are you accounting for all your accounts, like Savings, that you might be tracking in Goodbudget?
Without seeing your screen those are the first things I’d look at, but I’m fairly certain it won’t mean re-doing any of your hard work! 
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I have, what I believe, to be a similar situation - so a follow up.
Just started Goodbudget. I have included income from a prior month - so that my account balances match. However, this is showing up as “unallocated”. It really isn’t; it is my bank account money that I have used to pay my credit card bills. (I pay in full monthly.)
How do I exclude this money so it doesn’t look like I have “unallocated” money.
Again - I included them so my balances match. Should I delete them and somehow input a different balance? I just can’t wrap my head around it.
It sounds like you have a balance on your credit card that you intend to pay off with money that’s currently in your bank, is that right? If so, your Unallocated balance should equal the amount you owe your credit card(s). In that case, you’ll need to either input the individual charges represented by that balance in the envelopes where they belong and then re-Fill those envelopes from the Unallocated funds, or for a simpler method just make a single “starting out” transaction against the credit card (be sure its starting balance was zero so you don’t double up) and then just move money from Unallocated to cover it.
Here’s a very simplified example:
Bank account balance: $5000
Credit card balance: $1000 (owed)
Envelope allocations: $4000 (now Unallocated is $1000)
The transactions that are on the card but not reflected in Goodbudget will come up to $1000, so you’ll just input them individually or in aggregate, then cover those existing charges with an additional Fill from Unallocated.
Since theoretically a budget would start with perfectly filled envelopes and a credit card balance of 0, the difference here is that you need to account for the charges that were posted before you started using this app but which haven’t yet been paid.
I hope that makes sense! 
TLDR: You just need to “assign” the money in the bank to pay off the previous credit card charges one way or another.