Definitely a few glitches on this mission going on the evidence.
Last night I was playing through it online with my friend on co-op. We got to the part where you have to destroy the Covenant ship by boarding it. We had a slightly different problem where the ship was actually there, but we couldn't destroy the objective at the top. We disabled the shield it has covering it but no amount of grenades we threw at it would blow it up.
We even killed each other so we spawned with more grenades and went searching on the mesa for dropped plasmas, still wouldn't do it.
We had to go through the entire mission again after dashboarding, thankfully it didn't happen again so I guess you'll just have to take it on the chin and play through it once more.