macOS keeps track of which apps open specific file types. When Numbers is installed, Apple assumes you're going to want to open .CSV files in it, so macOS's internal database is edited to make Numbers the default app for that kind of file.

  To change this, Get Info (⌘-I) on a .CSV file in the Finder and perform the following:

1. under Open With dropdown, select a different app to open this type of file (TextEdit, BBEdit, SublimeText, Atom, etc.)
2. click on Change All... button
3. click on Continue

Safari does not post process files or transform them. It saves them exactly as the web server sends them or it throws an error code.

The worst thing Safari could do is decide the file is “Safe” and open it in the default application. You should disable opens safe files on Safari and then re-download the files in question.

Finder controls which apps open which file, so if you decide to re-enable “open safe files” be sure to chose TextEdit or another file to open .csv files or delete Numbers so that there’s no default Application for these files.

In more detail on the Finder opening - macOS keeps track of which apps open specific file types. When Numbers is installed, Apple matches all .CSV files to Numbers. To change this, Get Info (⌘-I) on a .CSV file in the Finder and perform the following:

1. under Open With dropdown, select a different app to open this type of file (TextEdit, BBEdit, SublimeText, Atom, etc.)
2. click on Change All... button
3. click on Continue