Yes. You get a stamp in your passport which will create issues in the future, when an immigration officer looks at your passport at an embassy or when trying to enter. You're also in the system as having overstayed.
Maybe you're the one is a bit challenged with English. Your sentence has two phrases, the first describing the expiration of the 45-day program, and the second one being a declarative statement "and will return to 30 days."
Did she show the visa, or say "work visa" at immigration when entering?
It's not that "immigration stamped her 45 days visa," it's that she didn't say anything to the immigration officer. Immigration officers can't look at every page of everyone's passport.
There are a bunch of videos on YouTube explaining the Thai evisa process. Watch a few, they're helpful. Make sure to watch more than one to make sure each part the person is explaining is correct.
If you aren't sure about something, you can always email the embassy staff via the evisa website. They should answer within a few days.
You need to compile pictures of all your passport pages with stamps/visas into a single PDF file and upload that. Make sure the images aren't too big, but still readable, since there is a maximum file size. Yes, the whole thing is not easy, but that's what it is at the moment.
You're a UK resident, so you can enter on a visa exemption, which since Oct. 1, will give you 45 days, with the possibility to extend for another 30 days inside the country. That will give you 75 days. You can leave the country and re-enter to get a new stamp. If you need 83 days, getting the Single-Entry Tourist visa would be better, since that would give you 60 days, and possibility to extend for another 30 days inside the country, for 1,900฿.
According to the Thai eVisa website, as a UK you can apply online.
