The message "some format is not compatible with csv.." indicates that the file contains some formatting that is not supported by .csv file.
Where does the .csv file come from? Can you use csvread() or xlsread() directly without opening the file in Excel? What if you open the .csv file with an text editor like M-editor. Do you see anything abnormal?
I suspect your .csv file has some problems. Use a text editor such as Notepad, Wordpad etc. to open it and visually inspect it to see if anything out of ordinary.
In MATLAB, you can use Excel COM server, go through a loop, open each .csv file and save it again. This is to utilize Excel to fix the problem. You probably can do that in Excel alone using Macros.
If you are using the Excel COM server, the following snip of code can be used.