This is obvious so I think I may did something wrong, but here are the steps to reproduce
At the beginning, there's 1 file in both alluxio and UFS, which is good
$ ./bin/alluxio fs ls /test
rw-rr- myuser myuser 0 PERSISTED 12-19-2018 10:49:58:851 100% /test/file1.txt
$ ll underFSStorage/test/
total 0
rw-rr- 1 myuser myuser 0 Dec 19 10:49 file1.txt
Now I create a new file in UFS
$ touch underFSStorage/test/file2.txt
$ ll underFSStorage/test/
total 0
rw-rr- 1 myuser myuser 0 Dec 19 10:49 file1.txt
rw-rw--- 1 myuser myuser 0 Dec 19 10:50 file2.txt
checkConsistency can not detect the new file, and the file is not in Alluxio
$ ./bin/alluxio fs checkConsistency -r /test
/test is consistent with the under storage system.
$ ./bin/alluxio fs ls /test
rw-rr- myuser myuser 0 PERSISTED 12-19-2018 10:49:58:851 100% /test/file1.txt