Intangibility: Has yet to be successfully developed, for most of the reasons given in the trope page (although I disagree on one major point: intangible objects can and probably should have mass; it’s the electromagnetic interaction they need to be lack in order to properly interpenetrate).
There is one prominent failure mode, however: muon metals, thanks to the Pauli Exclusion Principle, can pass through normal (electron-ic) matter as if it wasn’t even there, since electrons and muons do not mutually exclude. This makes life interesting if the magnetic couple necessary to hold the (muonic, due to the spectacular refractory properties of muon matter) magnetic nozzle of your torch drive in place fails, since you may well see said nozzle fly right through the rest of your ship and indeed you, impelled by the remaining coupled thrust. People tend to find this disturbing.
(Well, briefly, since a mere moment thereafter they tend to be preoccupied with the stern of their starship melting, vaporizing, and exploding, due to the ensuing catastrophic drive containment failure. And yet.)