Alpha - no way that I know of to prevent this. We actually wanted this for a long time b/c in earlier Versions of the AI there was a severe problem with them having NO queues filled. Now of course, we have the opposite problem b/c the AI is not checking their maintenance restrictions as to ships. I think this is supposed to be fixed in the next patch and could help the "multiple queue" problem you pointed out. Otherwise, you can make sure the exploration queue is minimal so that when it flips to the attack/defend queues (where they spend 95% of their time) there won't be problems.
Of course, the ability to call ships based on "design name" intead of "design type" would help alleviate this problem
