You have hit upon a basic mistake made by many fly fishermen. A squid doesn't move through the water the same way a shrimp, a minnow or a crab does. One of the most important rules in retrieving is that to make a realistic presentation, you need to manipulate your pattern in the way the creature you are imitating moves. This requires that you study the various creatures you're imitating with your flies.
Far too many anglers cast the fly and begin a standard stripping retrieve. For example, a crab swims at a steady, unvarying motion unless it is attacked. The best retrieve I know to imitate a swimming crab is to position the rod under your arm and then hand-over-hand retrieve the line in a smooth manner. Just the opposite occurs when you want to imitate a shrimp fleeing from a bonefish. In this situation, I would rather hold the rod in one hand and with the other, make a series of short, long, slow or fast strips.