Mission gates lock a path until the conditions to open that gate are met. For example, a class gate will only unlock if you have equipped a bot of the same class to your team.
Gates can cost anything to enter. Some can be open for a certain amount of time (like the remainder of a mission), and others can even be permanently unlocked once opened. Special keys can be found in specific missions to open certain gates.
You can see potential gates in the ENEMY CLASS BREAKDOWN tab before you enter a mission. A red gate means that you do not meet the requirements to unlock the path. You may also receive a gate warning if you do not meet the requirements to open a specific gate.
If you encounter a closed path in your mission, tap on the gate to view the missing resources needed to unlock it.