Randy,
I've encountered similar situations where siblings are baptized -or appear to have been baptized- in different neighboring localities. Some of the explanations are as follows: 1) The parish kept the records, and the name of the church where the children were actually baptized was recorded at margin. Often that information was not entered into LDS record, and only the name of the parish appears. Upon inspection of the actual image, the actual location of ceremony (baptism, marriage, etc.) can be verified. 2) Priest absence at a church (for multiple reasons). Accordingly, ceremonies had to be conducted temporarily in the neighboring town. Upon examination of the church books you would sometimes reference of such temporary absence and transfer of records. 3) People would choose to christen their children at different churches, for multiple reasons, including respective family ties of the father or the mother to the town where their corresponding families resided. Clues to this c
ome from records of relatives, or where the respective parents were born. 4) Individuals would move because of employment. I have records of relatives moving from one town to another, and then back to the original town. People look for oportunities today, and they would do the same in the past.
Check the original records (images) for clues. Often the names of the god parents are the same regardless of different localites. Also look for other records, including the marriage of the putative siblings in question. Multiple pieces of information can confirm that these are indeed are siblings.

Jaime Alvarado

It is within the realm of possiblities. While I am no expert, here are my
thoughts: Hopefully, someone already has these individuals in their family
tree and already have information, or have ready access to it, Are both
parents from San Juan de Los Lagos? Perhaps one is from San Diego de
Alejandria, or you might be able to locate siblings of theirs there, to
strengthen your hunch. Have you checked whether their is a Juan Antonio De
Anda and a Gerturdis Padilla marriage in San Diego?. But it is best to look
at the films to see what else you can learn. They may indicate grandparents,
where the parents are from, or have padrinos that are the same or ones you
know are siblings of the parents. I don't know when the Jalisco films will
be available online, but hopefully, soon!