I have some points in polygons green spaces and trees I want to intersect the data correctly, I try with Intersect tools but some data are missing and I do not why? the point layer is trees and polygon green spaces
First you need to make sure that both point and polygon data have the same projection. Therefore, if the both data have different projections, it may not give the desired output.
Then you can use select by location from Vector -> Research tools -> Select by location to select the point that intersects the polygon layer:
If you need more control on select by location tool, you can use the one located under the Processing toolbox -> QGIS geoalgorithms -> Vector selection tools -> Select by location: