Because the file has been handles manually, its 'archive' flag has been reset, because of this it is treated as "dirty" by Oracle.
$ export ORACLE_SID=[sid]
$ sqlplus
(Log in with user name "system as sysdba")
SQL> SELECT status,name FROM v$datafile WHERE status =! 'ONLINE';
(If any of the files are status 'RECOVER' do the following:)
RECOVER DATAFILE '[/full/path/to/file]';
ALTER DATABASE DATAFILE '[filename]' ONLINE;
COMMIT WORK;
SHUTDOWN IMMEDIATE;
STARTUP MOUNT;
ALTER DATABASE OPEN;
(Repeat if any more errors occur)
EXIT
