Obviously, filtering out zeroes should not filter out values that are not in fact zero. The problem here is that amateurs are working with Excel without understanding it. A finance department of all places should be well aware that the digits after the decimal point count, not matter how far after the decimal point.
But that is not the workplace problem. Well, it might be one, but one you didn't ask about.
There are two types of companies: those that think everybody can read their minds and craft a contract, so when that mind reading mysteriously fails, they can assign blame and make sure it's somebody's fault and someone pays. And then there are companies that collaborate and try to get the best result in an imperfect world.
The first type of company is left with a crappy piece of software that does not work, legal bills, court appointments and litigation over years and years. And all the time, their core business is running on broken software. Obviously they need a new contractor for each project, that again will not understand what they want, because not only are their mind reading capabilities limited, but they are new.
The other type of company will have a piece of working software for the requirements they had. They will improve on it or start another project with the contractor, that is now proven to do a good job and already has more experience in their business and their needs. While they might have gotten their software project for a higher price than the first company, the savings in lawyers and constantly changing contractors and the fact that their software actually works and they make good money in their core business makes it the better package deal though.
Your company is stuck in the first "contract & blame" mode. And that is systemic, it already crafted the requirements with "contract & blame" mode in mind. Because as you experience right now, it's not about fixing the problem, it's about who's fault it was and who needs to pay for it.
Good companies do not just put "requirements" out there. Good companies will have "acceptance tests" for each requirement, so that not only can you objectively test whether the software fulfills it, you can also test early and if the test shows that the requirement is not what was expected, you can change the requirement very early in develepment, where it costs very little.
As an example for your requirement, there should have been an acceptance test that read:
With the attached testdata.xls the process should frobicate 15 widgets, 13 of which are in yellow, 2 in red. 3 widgets will not be frobicated at all, because they will be filtered out.
And then when the developers run the excel file, it will be clear nothing is filtered out.
Then people will meet, talk and find a solution. Maybe the solution is to filter out everything smaller than $0.01. Or something else. Anyway, they can see how much it costs, it will probably not worth talking about the price, because two managers haggling over the price will cost more than the developer fixing it.
Point here is: there is no need for blame or finding fault, both parties did not think about this case, as evidenced by the fact that such a case was not brought up by either party as a test case.
Your company can either stay in "contract & blame" mode or they can start growing into a functional business and collaborate with their partners for mutual gain.
Acceptance Tests are one part of doing so. An open mind and looking at the benefits first, not the costs is another.