It is not error sometimes it happens whenever preparing receptor most important is that delete hetatm and water from receptor. after that you get +ve energy it means there is a possibility small molecule has low activity in the choose cavity. If small molecule does not show good binding energy it doesnt mean that small molecule is not reactive may be it possible that same molecule would be show good energy in another cavity. This is a hypotetical data you can get to evalute or screening for further study. and some times virtual screening is quite different from in-vitro or in-vivo study so go on check all the parameter and perform new job. Hope everything will be good.

Can you share the structure of the protein-ligand complex? Docking score on its own is meaningless.

There are so many factors to consider while answering this question. But you can check the following:

Does the protein have any missing residues at the docking site ?

Is the active site defined properly ? I.e the reactive part of the ligand with the protein.

Is the box size used fit inside the active site ? Different box size gives different results.

This should help https://www.bindingdb.org/bind/index.jsp in finding the nearest binding energy. Good luck

You can use Binding Affinity Prediction of Protein-Ligand (BAPPL) server to validate your result.

http://www.scfbio-iitd.res.in/software/drugdesign/bappl.jsp