During El Nino, the large scale pattern favors drier than average conditions over Central America and the Caribbean.  However, typical El Nino impacts are usually best seen in "seasonal" or an average of 3 months of data.  What you are pointing out appears to have been a significant, shorter-term weather event.  

Over the last 30 day average, here is the broader larger scale patttern as estimated by TRMM  (as of this posting, the dates are shown from June 9-July 8th 2015):

http://www.cpc.ncep.noaa.gov/products/fews/central_america/trmm_rainfal…

From this snap shot, most of the larger region is drier than average (i.e. consistent with El Nino).  But over Costa Rica, I see a wetter than average signal, which appaers to be mostly the exception rather than the rule.  

Overall, it is importat to realize that an El Nino does not guarantee impacts and there will be exceptions even during a stronger El Nino.