On occasion there are some minerals, this time flora (rather big one) that wont register for scanning.

I find that rather disheartening as there could be quite some interesting stuff that can be done with it.

Core issue:
dose not scan

steps to reproduce:
go on planet, look via scanner on everything until you have encountered something you can not scan (this dose occur on smaller plants and minerals as well)

expected behaviour:
all objects can be highlighted for scan and scanned. (not counting surface etc.)

This has been part of the design since 2016. The large flora and minerals that you refer to are treated in-game as being part of the planet as opposed to that which grows on the planet. This sometimes applies to trees, the large circular plants, a lot of the small shrubs, etc.

There may also be times when due to rendering some flora (or minerals) will not highlight and therefore cannot be scanned unless one shifts position, moves closer, etc.

Lastly, there are a couple of plants that can be scanned but do not count. This is a glitch or bug that appeared a couple of updates ago and applies to the sodium plants. There are, or were, a couple of other plants with the same issue.