A multiwire circuit by code MUST have both hot legs turned off by the same CB. If one were installed using 'regular' single pole CBs, that's an issue (as I understand the code, which could be wrong). So, having current flowing in a box when the CB is off means there IS a problem in the wiring, multiwire circuit or not.
In order for current to flow, there must be a complete circuit and a voltage potential. At your main panel, both the neutral AND the ground should be bonded together, so you should not get a spark when connecting them together at a remote point - that requires the two leads to be at a different potential, and the resistance of the wire should prevent that from being big enough to create a noticeable spark. This is MUCH harder to prevent with AL wire, though, as it's easy to get a poor connection if you do not follow all of the rules when making up connections. The ground wire is NEVER supposed to be used as a current carrying connection...it is there as a safety lead to provide a path to help ensure the CB or fuse will protect the circuit from an overload. Grounding things also can help with near lightning misses (a direct one would damage things, a near one, properly installed, might be survived without damage).