I just re-did my repro in ST3 without seeing any issue.
RTF is a pretty loose 'standard' of a file format so if you don't know the origin of them, it may be that they are just 'bad' RTF files.
If you open the RTF in a Word processor (e.g. Microsoft Word, Google Docs, whatever the Apple word processor app is..) does the formatting look 'right'?
If not - problem is the file.
If it is OK, try re-exporting (i.e. Save As or Save Copy to RTF format) from the word processor to a new RTF file, and then try that file in ST3 and see what happens. I.e. we're seeing if the word processing app can 'clean up' the file format.