I assume you're running this as the elasticsearch user, so there shouldn't be any problem there.
Exactly what did you run to get that directory listing?
If you ran the command that @ikakavas asked for:
ls -la elastic-stack-ca.p12
Then that output is quite strange - it would imply that elastic-stack-ca.p12 is a directory, which it certainly shouldn't be.
Alternatively if you simply ran
ls -la
then where is the bin/ directory from your original command
bin/elasticsearch-certutil ...
Something doesn't quite add up between the commands you say you're running and the output we're seeing.
You can try
bin/elasticsearch-certutil cert -v --ca ${PWD}/elastic-stack-ca.p12
which will eliminate any strange path problems and the exception message will be explicit about which file we tried to read.