I'm sure I'm not the first to say this, but I think your SD card is dying. They aren't sealed from dirt like hard drives are and hard drives die every day. I'd do my best to get all of the files off of the SD card, put them somewhere on your computer, then get a new SD card and copy all of those files back to the new SD card. It would also be a good safety thing to do with all of your SD cards, if you have data only on a card.
It's always a good idea to have a backup of any important data that you can't lose, so now that you have a card reader, you should be able to do that. When you get a project you're happy with, don't assume it's going to be there tomorrow. Copy the files to some folder on your computer and you can then rest easy that if that particular card goes belly up, you still have all of your data.
It's just one of the things you have to think about in the digital world. All of those SSD drives, flash drives and cards are wonderful and they hold a lot of data. But, just like a light bulb, they can work one day and the next day not work at all. And in your case, if you happen to save a file on an area of that SD card that is "iffy", one of those data access errors could be one of your files sitting on a bad sector of the card.
And with files like that, you need the file to be complete, to get your program to read it. I'm not sure if I would trust that card any more. Once it has a bad spot on it, I'd say it's only a matter of time before it gets more. I wouldn't even want to trust a sealed hard drive that has bad sectors show up. It's just not a good thing to trust your important data to.