Can radars detect all planes, including military ones?
Some military aircraft reflect little enough radar energy to be effectively undetectable. Note that the actual details are likely classified, but even the modern F-22 still has a radar cross-section of about the size of a steel marble. Still, the B-2, an older stealth aircraft, is claimed to disappear from air traffic radar when in stealth mode.

The same article on the B-2 also notes that it has "deployable radio antennas for navigation in civilian skies". When flying during peacetime and outside of an MOA, military aircraft generally have some level of coordination with ATC. If the pilots of a stealth aircraft don't want to be seen, then presumably they would be responsible for maintaining separation from other aircraft, as they cannot be tracked on radar. Of course, there's also plenty of airspace where aircraft don't need to talk to ATC at all (E and G in the US), and the pilot of each aircraft is responsible for maintaining separation.

That said, there are some things in this article that are unclear:


The Etihad aircraft received a TCAS alert for an aircraft that didn't show up for ATC. TCAS intentionally uses the same frequencies and signalling as ground-based secondary radar, so if an aircraft receives a TCAS response it should also show up for ATC. The article does note that the aircraft were "450 to 480km from Mumbai's coastline", so it's possible that the mystery aircraft just had a weaker TCAS response that wasn't received by a distant ground-based receiver.
The article suggests that fighter aircraft don't fly as high as 36,500 feet. A ground attack aircraft might not be able to fly that high, but most, if not all, air superiority fighters have service ceilings of at least 50,000 feet.