I don't cross shard much, so I may be incorrect. I have heard of a few gotchas when hopping shards.
The biggest being you need to keep your ticks going on both sides to get reliable transfers. An empty shard will often go to sleep and stop ticking.
Another problem is sometime the shards will have difficulty talking to each other. This can cause creeps to stuck in limbo for hours. As far as I've heard they all eventually arrive often in a single clump.
You may have stopped tracking your creeps too soon and the lost creeps are still in transit.