How to UNDO stopping OS X from writing Spotlight and Trash files?
What Metaxis described looks like it can be reverted with the following:

mdutil -i on /Volumes/yourUSBstick
cd /Volumes/yourUSBstick
rm -rf .fseventsd/no_log .metadata_never_index .Trashes
cd -


The first line with mdutil is the most important if you want your volume to index again, as it sets the indexing status for the volume back to on, according to the manual:

-i on | off
     Sets the indexing status for the provided volumes to on or off.  Note that indexing may be delayed due to
     low disk space or other conditions. 


EDIT:

in your case (but this is specific to OP), you forgot to cd (change directory) into the volume before deleting the index files and adding a few files. You just need to delete the files you created locally (in your home folder):

rm -r .fseventsd/no_log .metadata_never_index .Trashes


No need to use mdutil to re-enable indexing on your drive as you did the first command right and only did a mistake after the second command.