Missing Skills

Date & Time: 07/18/2019
World name: All worlds
Character name: All characters
Class/Level: All Classes and levels
Steps:
1. When playing as my Pugilist (Level 44, Conjurer (Level 31) and Arcanist (Level 16) characters, I noticed certain skills are unusable, such as the Conjurer's Protection spell, or Arcanist Energy Drain. I can't remember what was missing from the Pugilist because I already changed the unusable skills out for other class skills.

Question:
Is this a really glitch, or is this because I don't have any expansion packs, like the recent Shadowbringers? Are skills now dictated by which expansion pack I have?

That's working as intended I'm afraid (and is not a bug). Stormblood and Shadowbringers changed the game considerably in that with SB the old 'cross class' ability system was scrapped and replaced with 'role abilities' based on what role your class/Job is, and SHBs further refined that (and these changes are part of the main game and are automatically patched in regardless if you have the expansions or not). Long story short, a lot of abilities ended up being lost, either scrapped outright or changed to role abilities.

Either way, if an ability icon is greyed out and has a red line through it, sadly that ability has been scrapped and cannot be used anymore. There is no way around this unfortunately. And yes, Protect was one of them (it was first changed to a healer role ability, then it was scrapped completely). This page lists the details about the changes to abilities and the current ability lists for each class and Job.

So sadly, working as intended. :(

I see. I wasn't aware of any of this because I haven't logged in ages (I wish they at least kept Protect in). Thanks for clarifying.