Environmental Variables for OracleDB 12 in Oracle Linux are Overriding Each Other with SQLPlus Variables
I found a solution. 

I noticed that the path ORACLE_HOME wasn't working properly. I used a deductive method. I determined the error by executing common commands that normally run by supplying the name of the application (Within OracleDB suite). For example:

First I checked the oratab file, as follows:

 vi /etc/oratab


Which gave me the following output:

orcl:/u02/app/db12c/product/12.1.0/dbhome_1:Y


Then, I started executing common commands. For example, I ran the "Listener Controller application" as follows:

lnsrctl status


Which gave me the following error:

bash: /u02/app/db12c/product/12.1.0/dbhome_1/lnsrctl: No such file or directory


Then, I decided to use the command above by stating the path explicitly. 

/$ORACLE_HOME/bin/lsnrctl


Which gave me the following:

LSNRCTL for Linux: Version 12.1.0.2.0 - Production on 27-JUN-2017 20:28:22

Copyright (c) 1991, 2014, Oracle.  All rights reserved.

Welcome to LSNRCTL, type "help" for information.


Then I ran the status of the Lnsrctl, as follows:

LSNRCTL&gt; STATUS


Which gave me the following:

STATUS of the LISTENER
------------------------
Alias                     LISTENER
Version                   TNSLSNR for Linux: Version 12.1.0.2.0 - Production
Start Date                27-JUN-2017 20:28:37
Uptime                    0 days 0 hr. 0 min. 0 sec
Trace Level               off
Security                  ON: Local OS Authentication
SNMP                      OFF
Listener Log File         /u02/app/db12c/diag/tnslsnr/{ServerURL}/listener/alert/log.xml
Listening Endpoints Summary...
  (DESCRIPTION=(ADDRESS=(PROTOCOL=tcp)(HOST={ServerURL})(PORT=1521)))
The listener supports no services
The command completed successfully


After the above, I was able to run the commands normally. For instance,

sqlplus / as sysdba


Which gave me the familiar screen of:

SQL*Plus: Release 12.1.0.2.0 Production on Tue Jun 27 20:29:11 2017

Copyright (c) 1982, 2014, Oracle.  All rights reserved.

Connected to an idle instance.

SQL&gt;


And that was the problem. I'm not really sure if this is a glitch, setup problem, or design feature, but I hope this post can help someone who is going through the same situation. From now on, I have to use the command:

/$ORACLE_HOME/bin/lsnrctl


explicitly.

Thanks for everyone who posted.