It happens, but mostly because other formats don't produce usable CSV's. The biggest problem is if there are any free-entry text fields (common for customer/business name), and there isn't full quoting around these fields, base R will break.

I believe both fread and readr::read_csv do the right thing here, but the base-R perspective on data manipulation before read.csv is to use Perl (the R-core team are pretty old-school, to be fair).