Ragdoll physics can indeed interact unpredictably with animations that use IK (Inverse Kinematics). This is because both systems are trying to control the bones, leading to conflicts. Here are some points to consider:

1. Constraint Order: Ensure that the order of constraints is correct. Sometimes, the order in which constraints are applied can cause issues. You can check and reset the constraint order in the Spine Editor. More information can be found here.

2. Mix Values: You can reduce the influence of IK constraints by adjusting the Mix value. This can be done either in the Spine Editor or via code. For example, setting ikConstraint.Mix = 0; can help reduce the influence of the IK constraint when the ragdoll is applied.

3. Smooth Transition: If you need to transition smoothly from IK to ragdoll, you can use the SmoothMix method. This allows for a gradual blend between the animation and the ragdoll physics.

4. Setup Pose: When switching to ragdoll, you might want to reset the bones to their setup pose using skeleton.SetBonesToSetupPose(); to avoid any abrupt changes.

5. Independent IK Targets: Ensure that IK targets are not children of bones that are being flipped or controlled by other constraints. This can help avoid unexpected behavior.

6. Example Scenes: Refer to the example scenes provided with the spine-unity runtime, such as Spine Examples/Other Examples/SkeletonUtility Ragdoll, to see how ragdoll and IK can be managed together.

If these steps do not resolve the issue, it might be necessary to adjust your rigging or animation setup to better accommodate the interaction between IK and ragdoll physics.