A list of (most) things about the game that are not properly explained to the player:

• XP gain on level selection screen: not specified that it only affects profile XP
• Profile XP: never mentioned that it's only gained in Normal mode
• Custom maps: "drawing" mode for placing / removing tiles is only mentioned in old patch notes
• Custom maps: it's not clarified that excess resources mined are not given to the player after game ends
• Star research: it being impossible to complete is not obvious
• Trophies: it's not made clear that effects like "-0.5% towers upgrade price" (Cannon trophy) apply to all towers, not just the one the player got a trophy of
• Miner double speed: not explained anywhere in the game
• Towers: holding upgrade or ability button applies this action to every tower of the same type - never mentioned
• Detailed mode: mentioned only once in one of the tutorial levels, which people often don't pay much attention to
• Modifiers: players are often unaware of their existence even after unlocking them and often don't understand how to use them
• Score: its sources are never explained
• Maps: tile coordinates are not named (what is this random "3:17" in top right corner?)
• Missile: LRM is not explained
• Inventory: no mention of the "open 5 / 25 at once" functionality for chests and packs
• Inventory: 500 bases / portals cap is not mentioned
• Inventory: "hold to select" not mentioned
• Stage 6: gems are not explained at all
• Prestige: no proper introduction