Know your tools. When I see such headlines, I feel sad about the state of this world and obstacles to progress, angry about the stupidity of designing all the tools for the most lazy of users, and at the same time I also laugh about the failures of proprietary software and its users, who could easily have invested a little bit of time to learn alternatives, but apparently chose not to.
Yes the tooling they use might be terrible. It is your responsibility to either deal with the terrible tooling yourself, learn better tooling, or get a capable computer person in the room, who can navigate the tooling landscape and get you the results.
And of course, that is not even addressing checking your result yet. This is a sad state of the research landscape, often financed by public money, and then throwing money at MS for using a proprietary tool and messing up.
Working in this field, I think a lot of the issue is publishers often require small datasets in xls format for paper submission. So someone in the chain (corresponding author, editor, journal staff member etc.) opens the file in excel and saves it again.
Bioinformaticians are not doing their analyses in excel.
I think you’re reframing “when all you have is a hammer, every problem is a nail” into “when all you have is a screw and a hammer, it’s outrageous the hammer wasn’t designed to drive screws”.
A single tool must work for ever use case or should the tool be picked based on the use case? Tool X doesn't work for use case Y. Regardless of where you shift the blame, tool X doesn't work for use case Y holds.
Tools are designed for a particular use case/userbase. Excel was not designed for gene scientists. It wouldn't make sense for me, a home owner who uses a jigsaw to cut molding, to complain to a chainsaw maker that their chainsaw isn't right for my job.
Yes the tooling they use might be terrible. It is your responsibility to either deal with the terrible tooling yourself, learn better tooling, or get a capable computer person in the room, who can navigate the tooling landscape and get you the results.
And of course, that is not even addressing checking your result yet. This is a sad state of the research landscape, often financed by public money, and then throwing money at MS for using a proprietary tool and messing up.