So many Thais seem to think that padding a bank account is the right thing to do. As you've found out, it's the worst thing you can do but the myth seems to keep doing the rounds.
You now have a mountain to climb convincing an ECO that he/she should give your girlfriend a visit visa.
The first thing to do is fire the visa company and never use another unless it's an OISC accredited agency. It's simply better and easier to do it yourself with the help of the people on here.
IMHO the only way you can get around this is to explain that you used a visa company that gave you the wrong advice and then submit a new application showing the true figures from your girlfriend's bank account. You could explain that your girlfriend added a zero to the amount of money she intended spending while she was here. She actually meant 10,000 baht... That is only if she does have 10,000 baht of money she has legitimately in her account that she can account for.
It's a big mistake to supply a girlfriend's bank statements in the first place. Again in my opinion. For my girlfriend's visit visas we didn’t supply bank statements at all. All we supplied were the cash rental payments and the cash money she sent home each month and explained that she was paid in cash and the money was spent as soon as she received it.
The genie is out of the bottle now and I think she has to supply bank statements for any subsequent visa applications. How many months bank statements did you supply? It would have a bearing on when she next applies. You want to supply new bank statements that don't show the "problem" payments I think.