[Bug] graph-node allows deploying with features in manifest even when not used

Bug report

Graph node allows deploying subgraph with features labelled in features field in subgraph manifest even though the subgraph is not using that feature.

This gives misleading info about the subgraph.

Example Deployment: QmQ52Q83ovDZDKeLtUsTE6zzbWbwhXz8CnU9iGZKPzJdB3
When checking with index-node api, it returns, this subgraph is using grafting. But actually this subgraph is not grafted.

Relevant log output

IPFS hash

QmQ52Q83ovDZDKeLtUsTE6zzbWbwhXz8CnU9iGZKPzJdB3

Subgraph name or link to explorer

No response

Some information to help us out

• Tick this box if this bug is caused by a regression found in the latest release.
• Tick this box if this bug is specific to the hosted service.
• I have searched the issue tracker to make sure this issue is not a duplicate.

OS information

None