The main disputes with Irún concerned the loading and unloading of goods, demolition of constructed houses, funerals of royal persons, imposition of local taxes (sisas), delivery of allocations, military services, inspection of weights and measures, and exemption from jurisdiction.
This same town, along with Lezo and Pasajes de San Juan, had further disputes with Fuenterrabía regarding the military service of their inhabitants on the following occasions, according to Gorosabel:
“They arose again in 1615 on the occasion of the delivery of Infanta D.ª Ana and Princess D.ª Isabel, and the apparatus that the French intended to place on an island in the river; but those that occurred in 1617 were even more serious. Two criminals, attempting to cross into France, embarked on a barge in the Fuenterrabía area; the town’s alcaldes, informed of this, ordered the provost, with six companions, to arrest them in a small boat. Upon reaching the Endaya side, they were attacked by the townspeople, captured, mistreated, and their boat was burned. The people of Fuenterrabía took five Endaya residents as ages, and having seized five barges from Endaya, they burned them completely. These first incidents led to mutual reprisals, such as the seizure of French ships in the port of Pasajes, and the imprisonment of several Fuenterrabía residents by the military governor of Bayonne.
At the same time, the French placed a large mast on one of the islands of the Bidasoa River as a sign of possession. Consequently, the alcaldes of Fuenterrabía, with one hundred armed townspeople, went to the site, tore down the mast, and burned it near the marketplace in full view of Endaya. The Spanish and French governments were informed of all these events; thanks to their intervention, the disputes were resolved with the return of prisoners and ships.
Upon the death of King Felipe III in 1621, the province decreed that all towns should hold his funeral with the utmost solemnity; and that the following day the banners would be raised for the majesty of Felipe IV. In accordance with this decree, Fuenterrabía set the day for both ceremonies and sent a mandate to the towns of Irún, Lezo, and Pasajes for their residents to come armed and in mourning. These three towns did not feel obliged to comply, considering it contrary and offensive to their civil status. They attempted to excuse themselves and sent their respective councilors, Cristóbal de Zumarrista and Vicente de la Torre, to Fuenterrabía to explain the reasons for their absence.
The councilors of Fuenterrabía were not satisfied with the explanations of these two commissioners; on the contrary, they arrested them and imprisoned them in the public jail. The commissioners appealed this arbitrary action to the provincial corregidor; although he ordered their immediate release, without prejudice to the outcome of the case, his order was not obeyed. After twenty-three days of strict imprisonment, the matter was resolved by a concord agreement uted on June 14 of the same year. In this agreement, the towns of Lezo and Pasajes promised to attend Fuenterrabía on all such occasions and for any service to His Majesty, as they had customarily done before. Fuenterrabía, for its part, discontinued the criminal proceedings that had been initiated.”