They must have had disagreements, but of what kind were they?
Paul Preston claims -- convincingly IMO -- that Franco was full of enthusiasm for joining the war in 1940 but that a combination of Nazi hubris, Von Ribbentrop's ineptitude and an inability to reconcile Spain's desires with those of Vichy France caused him to reluctantly change his mind.
Spanish assistance to Germany sometimes far exceeded that permitted by its neutral status, for example by allowing U-Boats to refuel in its ports.
This fact was cleverly exploited by the British in Operation Mincemeat: a corpse carrying fake documents was dropped in the Mediterranean Sea at a point where it was known it would wash up on the Spanish coast. Spain passed the misleading documents on to Germany resulting in a major strategic blunder on Germany's part.
I don't know of any sabotage. The Nationalists got help from Germany early in the war with airlift capacity they didn't have--which was critical in getting the Army of Africa to the Spanish mainland. Later, the Condor Legion supplied a potent air force and a small ground continent that were quite useful for the Nationalists. In return, the Germans got trade concessions from the Nationalists, were able to try out their equipment and tactics without risking a full war, and undermined French and British security by removing the Republican government in Spain (which was much more friendly to French and British interests). There were minor squabbles about the conduct of the Spanish Civil War (particularly Franco's plodding advances rather than looking for knockout blows), but nothing major.
Hitler did want Franco to join WWII, but Spain never did. There was a Spanish "Blue Division" that fought on the Eastern front from 1941 until the beginning of 1943, but it was withdrawn due to pressure from the Allies, conservative Spaniards, and the Catholic Church. Germany did get Spanish iron ore and other goods during the war.
Basically, both Hitler and Franco used each other to further their own ends. Neither was particularly overjoyed with the other, but they weren't enemies either.