From what I’ve read because we gave notice to marry in February & my fiancé returned home, she should have then applied for a spouse visa because you cannot marry on a tourist visa which we did in the July.
First off, you cannot apply for a spousal visa unless you are already married BEFORE you enter the UK, so that would have been the wrong visa to apply for anyway.
Secondly, while you aren't supposed to marry on a visitor visa, if UKVI gives you permission to do so, then it's perfectly fine.
Technically, if you know in advance that you plan to get married while visiting the UK, then you should apply for a Marriage Visitor Visa first, so that you will have already been given permission to marry in the UK before you arrive. So, when you came back the second time, you probably should have applied for a Marriage Visitor Visa first, but since your application to marry had been approved, there was nothing stopping you from marrying on a regular visitor visa.
However, it's all done and dusted now, and how you got married is no longer relevant.
As I said, for the spousal visa, the only things that are important are that the marriage certificate is valid and legal, and that your relationship is genuine.
We’re worried that UK immigration will look for any excuse to bank a few grand for misleading immigration.
Nope, they won't do that, because you didn't mislead immigration. You asked for permission to marry as a visitor, and it was granted. End of story.
You got married legally as a visitor and returned to the US afterwards to apply for a spousal visa... and there's nothing wrong with doing that. Several people on the forum have married in the UK either as a regular visitor, or on a Marriage Visitor Visa, then returned to the US to apply for a spousal visa, and their spousal visas have been granted without any issue whatsoever.
I can imagine they see from our marriage certificate we married in England, but no application on their system for a marriage visa 
a) they probably won't be able to see that anyway, because it's up to you to declare any previous visas you have applied for on your application form
and
b) they already gave you permission to marry without applying for a marriage visa anyway, so there's no issue there.