There are 5 mains highways that connect Portugal and Spain. Then are around 15 (can't find the details, from memory) that are normal roads where you can also do the crossing. Then you have several smaller roads you can also do the crossing. If you are really really into it, then you can also cross it by walking in several other places.

Having 24/7 border patrol between two land connected countries setup and agreed over 20+ crossing points isn't something easy to do, specially during a pandemic where those agents are also needed elsewhere (and there were border patrols along the mains roads, but not close to all).

Compare to only entering by airplane where you can a) prevent planes from landing by just sending an email (exaggerating) and b) anyone that lands goes through a funnel where you can easily quarantine them.

And you can't compare a city, with 1,285 km2 with a country of 92,212 km2 (and other countries even more) and talk about border controls. Portugal also did the same to a city with some success but still there were flaws in the patrolling.