There are many combinations of upgrades and guns that may be more effective against each other. Typically, certain guns counter each other, but the skill, play-style, and upgrades of the user can alter the outcome dramatically.
Below are a few of the common or technical counters (the facts are straightforward).
Sniper beats LMG The sniper takes three shots at most to kill a player high health and armor. LMG users suffer at range due to the low movement speed and low range, allowing a competent sniper to kill them quickly.
Shotgun beats sniper: The shotgun is a relatively light weapon, allowing the user to rush and take cover.
Skilled players can kill other players regardless of their weapons, but the above aforementioned are the general weapon advantages.