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This would be the expected behavior for any teleporting ships, actually -- teleporting ships arrive at their destination, whatever that is, instantly. If you want engineers that follow along as part of your main fleet, you don't want teleporters unless your fleet itself is also teleporting. That's the one bad thing about using teleporting engineers.
On the plus side, there are regular mark I engineers, or mobile repair stations, which would act just as you would want. If you're set on using teleporting engineers, then I would leave them behind in reserve, and then move them forward to repair only once the coast is clear. Engineers are not particularly effective in the thick of battle, anyway, because they can't repair anything that has been shot within the last 3 seconds.
Hope that helps! Others might weigh in with how they use these, too.