the bio-hazards of pallet wood
If there are hazardous chemicals used in shipping, they are closely monitored and any spills must be reported internally to the shipper and to a HAZ mat agency. That agency comes in a cleans up the spills and will destroy or remove the remains. Other chemicals like solvents or oils will not be a hazard to your health, unpleasant maybe.
To get to the bottom of this issue, I would talk to the company who is disposing of the pallets and see what their policy is and what products they provide that were shipped on them. If this request is denied, then move on down the road and find a different source.
there are many manufacturing companies locally here that use pallets and shipping containers, some of which are set out on the curb for the taking. Typically they are metal machining, stamping, tool and die, welding fabricators etc. which just use the pallets to assist in trucking them about with forklifts. I would have no issues using these personally.
The answer to your question will only be as detailed and specific as the question is detailed and specific. Good questions also include a sketch or a photo that illustrates your issue. (:< D)