I got kind of the same problem.
The weird extra bytes at the beginning of CSV answer from the API are causing a lot of tools to crash or say the file is broken.
Also, the encoding is not UTF-8 and I need to convert it. And I have a problem with line endings too, which might be linked.

I end up writing a PHP script getting the PHP serialized export and creating the CSV myself :-/

We found a fix after changing two defaults in the file Csv.php in the Piwik package.
Filepath: ~/piwik/piwik/plugins/API/Renderer/Csv.php

In line 34 $convertToUnicode = Common::getRequestVar('convertToUnicode', true, 'int', $this->request);
change true to false and

in Line 57 Common::sendHeader("Content-Type: application/vnd.ms-excel", true);
change application/vnd.ms-excel to text/csv

We changed the content-type first, but that didn't help with the extra bytes (a UTF-16 BOM, I think). Changing the convertToUnicode flag worked.

However, we didn't reset the content-type to the default before we changed the flag. That means we didn't exactly isolate the problem, so I can't say whether this is solely a unicode issue or whether the unicode flag and the content-type default are interacting somehow. If we have some time in the next few days, I'll see if we can test it.

Thanks for the suggestion. Maybe we could improve this in Piwik 3.0.0! I think it's very important that CSV export create CSV files that work well for all tools. But we need to make sure our CSV files can also contain unicode exotic characters (which is the reason we have implemented this 'convert to unicode feature')

Thank you for the report 👍 To likely fix the issue, could you upgrade to the latest Matomo version?
see https://matomo.org/docs/update/

if you still experience this issue afterwards, please re-open this and post a comment. Thanks!