Subgraph: Missing wires and random nodes with red borders after 2-3 workflow runs

### Description

After running a workflow 2-3 times, subgraphs become visually corrupted: wires/connections go missing, and random nodes appear with red borders inside the subgraph.

### Steps to Reproduce
1. Create a workflow using subgraphs
2. Run the workflow 2-3 times
3. Observe that subgraph rendering becomes corrupted with missing wires and red-bordered phantom nodes

### Expected Behavior
Subgraphs should maintain their visual integrity across multiple workflow runs.

### Actual Behavior
After 2-3 runs, wires disappear and random nodes with red borders appear inside subgraphs.

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*Split from #9979. Reported by @gifandy*

┆Issue is synchronized with this [Notion page](https://www.notion.so/Issue-9999-Subgraph-Missing-wires-and-random-nodes-with-red-borders-after-2-3-workflow-runs-3256d73d365081d08c74d98b63183315) by [Unito](https://www.unito.io)