Jim's 106NY papers do refer to "Hubbard" more than once - but his actual enlistment papers to the 106NY show "Hobart M. Walker". It is the same man. So this is his unit history:
44th NY Infantry. In 8/30/61 Co. A; Sgt., Co I 9/25/62; wounded/captured Malvern Hill 7/1/62; paroled (when? where from?); discharged for disability 11/16/62
12th NY Cavalry. Mustered in 12/18/62 - discharged 6/23/63 without being commissioned 2nd Lt.
150th OH (100 days) Co. D 5/2/64 to 8/23/64. Garrisoned Washington DC forts during Jubal Early's raid. Hobart was mustered out with the company in Cleveland - possibly Camp Taylor.
106th NY (1 year) enlisted 27 Sept 1864. Was assigned to detached duty in Company C of the Permanent Party on Hart's Island.
Hart's Island was a gathering place for recruits. The Permanent Party was their escort to the front and was composed of men detached from their own regiments (as was Hobart). Under an officer, a group of PP soldiers would travel by ship to the front making sure the new recruits didn't skip off. The PP would then return to Hart's Island for the next assignment. Hobart (his papers show) died on the Lyon while returning to NY from escorting recruits to Wilmington. It is possible that they composed the returning ship's guard, since there were at least two Confederate soldiers on the fatal voyage.
My thought is that perhaps Hobart and 21 other Permanent Party soldiers are mistakenly listed(some duplicated) in the Lyon passenger list as "22 recruits" under an officer. They were not recruits but recruit escorts. There are other Permanent Party soldiers on board the Lyon and I suspect some of those "unassigned" to a company in various regiments were in fact on that detached duty.