Hi,
I'm the developer of MindNode and Hampshireboy mentioned this discussion in a support request and I hope I can shine some light on this issue.
iOS 9 added a new feature called "Open in Place". This means instead of copying documents into an other app's container, the receiving app can edit the document directly and the user doesn't end up with two copies of the document. MindNode adopts this new behavior. Unfortunately Apple so far doesn't support this and any other iOS 9 feature (including multitasking) in their iWork apps.
We think the problem you are seeing related to Keynote (and any other iWork app) is most likely related to the iCloudDrive.app thinking MindNode is the most likely app installed on your device capable of opening Keynote documents. The reason is that the MindNode and Keynote file format is very similar. Like Keynote we use file packages and thus inherit from the same base UTI. When iCloudDrive.app tries to find an app to open a document, it scans it's registered UTIs, sees that MindNode most likely conforms to the UTI and sends the Keynote document to it.
There is sadly no solution for this issue and we have filled a radar for this bug with Apple. And AFAIK even if we remove this feature, you would still always get the "Copy to Keynote" behavior from iCloudDrive.app until Apple fully supports "Open in Place".
The best workaround we have found is this:
1. Long press on the document in iCloudDrive.app
2. Select info from the menu
3. Click the action button in the toolbar to bring up the share sheet and select "Copy to Keynote"
Sorry that we are currently unable to provide a better solution.
Markus