Overspent Azure Credits

I am the CEO of a small scale startup that decided to use Azure for our backend since we got accepted into the Microsoft Startup Program and got the $1,000 in Azure credits. When we started on Azure we set up spending limits on Azure and a few days back we applied for level 2 of the Startup Program which would give us $5,000 in Azure credits. Just yesterday we got charged with a $2k bill for the previous billing cycle on our card with a $1k bill already for the coming billing cycle. For now we have scaled down our backend to the absolute bare minimum but I would like to understand what our options are regarding the $2k that has already been charged onto our credit card.

I worked with our CTO to set up spending limits and yesterday when we checked we didn't see those so we probably made a mistake while setting them up. $2k is a lot of money for us at this stage and we don't have the budget to be able to afford this (for reference our entire monthly budget right now is $1.2k). Can we email Azure, explain our mistake and ask whether we can get the money refunded to us and take it out of the credits we will get in the next round? How understanding is Azure in cases like this? We expect that we should be accepted into level 2 of the Startup Program by early next week at the latest.

Edit: I had originally written this post a while back for another forum so some of the details stated above are not valid any more. We have since been accepted into level 2 of the Startup Program and have received our additional credits but are still being billed for the $2k on our card and we need to pay off our card for that on the 19th. Also, we have an additional $1k in charges that will be charged to us on the 21st and it doesn't seem like the credits are applying to that charge either. We are able to view and confirm that the credits are in our account. Would appreciate any help and/or advice to resolve this issue.