Clip tool giving strange output outside scope of features to clip

[LauraGuthschmidt]

I have a layer with Shapefiles (see image shofiles), and a layer with mangrove coverage (see image mangrove deforested). I only want to keep the mangrove coverage where it is within the boundaries of one of the shapefiles, so I used Clip to clip the shapefiles from the mangrove layer. This works like intended, except that some parts are not correctly clipped, there is mangrove coverage within shapefiles that is not kept, and there is data kept that falls outside the shapefile boundaries (see image clipped mangrove).
Can somebody tell me what is going wrong?

[DavidPike]

That's strange. Can you take a screenshot of your clip settings?  Are they in the same projection/CRS?

[LauraGuthschmidt]

Thanks David. I have set the extent to multiple settings to see if that would make a difference, but it came out the same for each try.

[DavidPike]

what about the CRS for the input features and clip features?

[LauraGuthschmidt]

Both are in GCS_WGS_1984

[Robert_LeClair]

Laura - do you shapefiles have a *.prj file for both of them?  If they're in different projected coordinate systems, have you set the Geographic Transformation?  I would also try exporting the shapefiles to file geodatabase feature classes and redo the workflow.  What is the result?

[LauraGuthschmidt]

They both have the .prj file. I have reprojected one of the layers to GCS_WGS_1984, so they are the same. When I tried exporting them to geodatabase features, the clip tool only generated empty output, while the extent was set to default

[Robert_LeClair]

Hmmmm...interesting.  Are you able to share the data with us in this thread so I can work with it in my ArcGIS Pro for testing purposes.  If not attached in the thread, my email is rleclair at esri dot com  Thx!

[Mary_Murphy · Accepted solution]

Project to a local projection [PCS] > add the projected layers to a new map > perform the clip.

Ensure that in the Clip environments the output coordinates are the same projection as the inputs layers.

[LauraGuthschmidt]

This worked perfectly, thanks!