where a small group of the investigator strongly disagree with the findings and issue a minority report, has that ever happened with aircraft crashes.?
As far as I know aerospace was the first industry to include this industry wide as a standard option.
Happens on a regular basis. The minority report as you call it is included in the final report. You can read about it in ICAO Annex13. In many cases various parties include some comments. In NTSB cases you can find minority opinions of individual NTSB members. US military cases have a similar approach.
Some high profile dissent cases:
EgyptAir990 is a case. It crashed in international waters, which put Egypt in the lead. But Egypt delegated to the US NTSB. But in the end disagreed with the NTSB report and the Eqyptian report was included in the NTSB report.
In a similar Indonesian case, Silk Air 185, the Indonesians took the lead, the NTSB was a party. And here the NTSB disagreed with the Indonesians. The NTSB also published a 'findings' report.