Yeah, I have the same issue with a 4-3-3-0. If you're anything like me, then your CC are often coming from fast through balls, long balls over the top, low crosses from one wide player to the AM/other winger or runs from your wide players, all of which are deceptively hard to score from. In other tactics, a CC is often a player being put through on goal, getting a completely free header or something relatively simple, but when you're playing with a strikerless tactic your chances are often from difficult angles and at high speed. The stats are misleading in that way: I would say that a good 30% of what the game classifies as CC for that kind of tactic are basically half chances. Sometimes you just get bad luck as well: I had 5 CC vs Spurs in 25 mins last night and ended up losing 2-0, despite Soldado getting sent off 30 mins into the game.
I can't say why you're conceding without looking at your tactic, but if you're using ramdeuters or IFs then your opponent's fullbacks will often get a lot more space. Given that the game is currently very iffy on defending crosses that could explain your problems at the back.