libmwiptutil.so: cannot open shared object file: No such file or directory

I faced a similar problem to https://www.mathworks.com/matlabcentral/answers/110963-invalid-mex-file-root-mcrcache7-17-autobl0-toolbox-images-images-private-imhistc-mexa64-libmwip when I upgraded our application from 2013b to 2016b. I found the libmwiptutil.so file in mcrCache and if I add that directory to LD_LIBRARY_PATH it is working. but the cache is not filled until the first run (which fails) and I don't think adding cache path to LD_LIBRARY_PATH is a good idea. mccExcludedFiles.log has just these (addInstalledToolboxesToJavaPath.m, addInstalledToolboxesToPath.m, addInstalledZipAddOnsToPath.m, pathdef.m, initdesktoputils.m) and the file exists in the ctf in the produced testing folder. I should note that I am using the redistribution_files_only, I install mcr and update the jar file in the target machine. What is the correct way of fixing this?