Why does excel always say "..may contain features that are not compatible with CSV" when saving a CSV file?

Microsoft Excel will claim this when saving to just about any format other than .xls or .xlsx. The reason is that only these (proprietary Microsoft) formats can support Excel features like formulas, (conditional) formatting, charts, multiple worksheets, etc.

If all you're saving is data, you can safely ignore this message. I think you can even tell Excel to shut up and stop telling you that with a little "Don't show this warning again" tickbox on that "error" message.

To the person criticizing "your" CSV formatting, I'd shoot back that it's Excel, not you, generating the CSV file, so any error in the CSV format is Excel's error, not yours.

Looks like there is a way to fix this, I just found this article, which worked for me using Excel 2013.

Registry subkey 
HKEY_CURRENT_USER\Software\Microsoft\Office\14.0\Excel\Options
Value name  DisableSaveAsLossWarningOpenDocumentSpreadsheet
Value type  DWORD
Value data  0 - Display the warning message
            1 - Suppress the warning message

The registry value changes to

DisableSaveAsLossWarningOpenDocumentPresentation for Powerpoint and
DisableSaveAsLossWarningOpenDocumentText for Word

The features that Excel is complaining about are settings and functionality like cell formatting, column filters, formulas, and other Excel specific functionality that won't be saved when you save to a CSV.

For example, if you had a cell that contained a formula, such as =2+2, only the evaluated value of 4 would be stored in the CSV, the formula itself would be lost.