To summarize some other discussions about this, it is important to note that funds in the other category must be used for the purpose they were intended (per the financial audit). The "Other" account at the bank doesn't itself have subcategories, but we are asked to make subcategories in our local MLS so that members can pay for some service, usually scout or girls camp if needed/approved. However, on the "banks" books, this just looks like money in the general "Other" account, the bank doesn't have any subcategories.
To get a negative balance in a subcategory means funds were taken out of the bank "Other" account generally, and by necessity, they were taken from donations that were intended for a different purpose, meaning, your boy scout other subcategory fund might pay for your girl scout camp, as the money had to come from somewhere.
As described, the way to correct this is to pay out of your budget to get the balance back to zero in that other subcategory that was negative. Alternatively, you could have people who benefited from that service pay to that other fund to get it back to zero.
There is a part in the instructions that talks about "not jeopardizing" the charitable status of the church. "Other" donations are not charitable donations, because they are specified for a purpose (the donor can influence how the funds are used) and may directly benefit a person or the donor. In the US, this does not count as a charitable donation, and the church does not have to report it as a charitable donation (as I understand).
However, if the Bishop or anyone else were to use the funds for a purpose that the donor didn't intend, it might become a charitable donation, and might require the church to report it as such. I don't know for sure, but I believe this is why the church instructs us that funds paid to the other account should be returned back to the donor if they aren't used for the intended purpose. It also explains in some respects why a negative balance in an other account is a problem on the church audit, as the only way to get that is to use funds out of the other account, which means they are not used for the intended purpose, and implies the church should report that for tax purposes. Again, this whole last paragraph is somewhat speculative, but it could well be the case.