What was the point of tension between the Franciscans and the other institutions of authority that reduced the effectiveness of managing California?

Spanish Franciscans coming from the Viceroyalty of New Spain built a series of Missions along El Camino Real or the Royal Road in Alta California from 1769 through 1833 with the objective of converting the local hunter-gatherer populations to Roman Catholic Christianity and town life based on settled agriculture and animal husbandry. The 21 Missions that ran from San Diego to San Francisco also instructed the natives in carpentry, masonry, blacksmithing, tanning, candle making, wine making, and music.
These Catholic Missions prospered until the Viceroyalty of New Spain succumbed to Mexican independence in 1821 their rich lands became objects of envy for the Mexican Californios. The Mexican government began the emancipation of the natives in 1826 with the intention of granting them mission lands and Mexican citizenship, but without the structure offered by the Spanish Franciscans, the plots were soon abandoned by the natives who had by now lost the skills necessary to maintain their former hunter-gatherer lifestyle.
As Spain would not recognize the Mexican government, the Mexicans determined to drive out all of the Spanish under the age of sixty further increasing tensions between the Spanish born Friars and the new Mexican government. The Mexican Governor did intervene on behalf of some Franciscans when the law took effect, but the Spanish Franciscans were soon replaced with Mexicans loyal to the new government in Mexico City. Although Governor Figuroa in 1833 originally intended to maintain the Mission system, the Mexican Congress passed new legislation requiring the secularization of the Missions and the way was now open for the destruction of the Mission system which soon began in earnest. The decrees of confiscation began in 1834 and without the extensive mission lands and buildings (only the chapels were exempt) necessary to maintain the complex mission economies, what little remained was quickly abandoned by the natives and remaining Franciscans and quickly fell into ruin.
The largest tracts of land were acquired through land grants by the main Californio families that had influence with the Mexican Governors of California, and the era of large Mexican cattle ranches replaced the more diversified and advanced economy of Spanish California.

Catholic priests of the Franciscan order established missions for the Native Americans in the late 1700s until 1833 in the province of Alta California. The Franciscan's goal was to convert California’s original inhabitants to Catholicism and assimilate them to the European way of life. During this time period, the Spanish Empire ruled the area. Many Native Americans were intrigued by the mission settlements, called reductions, but once they were indoctrinated into the mission compound, they were often forced to stay. In 1810, Spain lost power of the area when the Spanish king was imprisoned by France. Money and support from Spain ceased. Mexico achieved its independence from Spain and took over the area. However, the missions still appeared loyal to the Roman Catholic Church in Spain. Worried about the mission’s lack of loyalty, Mexico passed “An Act for the Secularization of the Missions of California,” which took away the mission land and organized it into grants called ranchos that were given away or sold.