OK so what I would do in that case is not remove the transaction, but add an additional one for the money coming back in. Then categorise the transaction as "Savings account" or something. If you categorise both the outflow and inflow as the same thing, the effect will balance at 0.
I don't know why it's given you an extra £100. If you look on the web rather than mobile, you can see things like recent moves which will help you figure it out. It might also be that some category is now £100 (or £200? £300-200=100?) overspent which will reflect in To Be Assigned.
Another option is to add the savings account to YNAB, maybe as a tracked account rather than a cash account. Then you can just tell YNAB that was a transfer to/from X account.
For the payments which come out early, move the money from August back to July and then they won't look like they are overspent. Fund September 1st's transaction in August going forward. Consider changing the date of the transaction to the 28th to reflect when it actually comes out.
If you paid it on 28th July then it didn't come out of August's pay, because today is only the 1st, and you had to physically have the money in your account on 28th July. YNAB does not want you to allocate spending to paychecks anyway, YNAB wants you to think about having all the money you have right now today in a giant pile and allocate it into smaller piles. Having certain payments allocated to certain paychecks is more of a Mint or similar kind of budgeting mindset, which is a different method.
Because DH gets paid on the 25th and we have a few payments which come out on 28th/30th/31st, I do tend to "save" those, so for example the July 30th payment I only fund after the July 25th payday. I try to fund 26th Jul - 25th Aug with that 25th July paycheck.
Ideally according to YNAB you should fund the August 30th payment with the July 25th payday, but because we have some fairly beefy payments coming out on that day it's just not something I've prioritised.