If you have problems unlocking this achievement, read this solution!
I had the same problem. I had two players with 50+ goals and no achievement. Both players where defaut players that I've got at the start of my FUT Team. I then used a pack player and when I scored the 50th goal with this player, the achievement unlocked!
FIFA 12 had a similar achievement that was glitchy if the player wasn't pack pulled, so use a player you got from a pack just in case. If you have the problem in FIFA 16 that the achievement won't unlock, use a player from a pack.
Please let me know if this solution works for you too! Thanks!