When you did the glacier operation, the GUI was telling you that it was COPYING the files to glacier. Those files also existed elsewhere, in normal S3 space. There's ways to cure this issue at the command line, primarily a list of all attributes per file - and there you can see the respective storage plans.
Secondly, do you have billing alerts set up, at 1.25x per average day's accrual? (30$/mo would be around $1.25/day, as not to email-bomb you). Billing alerts would NOT have solved the issue of improper storage class, but you would have seen a massive spike in costs. It probably would have cost you maybe $100-$200 to solve it early on.
Thirdly, how much of the 5 Pillars of Well Architected Framework are you following? ( https://aws.amazon.com/blogs/apn/the-5-pillars-of-the-aws-we... ) Admittedly some of these are "pay AWS double and get disaster prevention" style rules. However... pillar 5 is all about cost optimization. An ounce of prevention is worth a pound (or $7k) of cure.