Can someone explain why we would skip the side mission after doing a forced mission? The rules say play the next available campaign stage which would theoretically still be the side mission wouldn't it?
Forced Mission
Correct. You would play the next mission listed in the campaign log. That may be a side mission or a story mission, they are all part of the campaign.
Forced Missions don't count towards the progression on the main campaign stage, If you look on the campaign tracking sheet, they have their own little area. After the Forced Mission has been resolved, you pick up right where you left off in the campaign stage.
See "Forced Missions", RRG, Page 17:
Forced missions are resolved between campaign stages. After resolving a forced mission, players should perform the “postmission cleanup” step of a Mission Stage. Then they resolve the next available stage of the campaign.
If the mission occurs immediately after another mission is resolved, they resolve “post-mission cleanup” but do not resolve any Rebel or Imperial Upgrade Stages before this mission. The threat level for a forced mission is equal to the threat level of the most recently played mission.
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Can someone explain why we would skip the side mission after doing a forced mission?
You don't. Forced Missions interrupt the normal mission flow and add to the mission total for the campaign.
Maybe you confuse it with Agenda Side Missions which are played as a Side Mission (and thus deprive the Rebels of one of their precious Side Mission slots)?