Tomo - 

Is your study area a box?  If it is then you don't have to use rxtractogon, you can use rxtracto_3D and just input the lat and longitide ranges.   I realize this doesn't address you primary question - I am checking into that now.  

Cara

so you can simplify it as

xcoord <- c(-123,-115)
ycoord <- c(28,36)

chla.MB <- rxtracto_3D(dataInfo = data.Info.MB8day, 
                        parameter = parameter, 
                        xcoord=xcoord, 
                        ycoord=ycoord, 
                        tcoord=tcoord.MB, 
                        zcoord=0)

Your time dimensions requested data outside of the range of the dataset.  Here is code to extract the ranges of the dataset from the metadata (this code is also in Chapter 4 of the online R exercises). Note you modified slightly the name of your dataInfo so you will need to take that into account in your code  

# Extract the beginning and ending dates of the dataset from the metadata in dataInfo
global <- dataInfo$alldata$NC_GLOBAL
tt <- global[ global$attribute_name %in% c('time_coverage_end','time_coverage_start'), "value", ]

# Populate the time vector with the time_coverage_start from dataInfo
# Use the "last" option for the ending date
tcoord <- c(tt[2],"last")

Also I just ran the code and it worked for me and downloaded all the data. Our erddap is being a little flakey this week, and that might have been why it failed.  Try running the code again.   

Different datasets have different attributes that might require slight alterations to the call. Changing datasets can mean that the varabale name changes. Chlorophyll can be expressed as "chlorophyll" , "chl", "chl_a", "chlor_a" etc.  Sometimes the dataset has an altitude dimension which must be accounted for. Longitude can be expressed as -180/180 or 0-360.  All of this can be determined by looking at the information returned by the dataInfo call.    Come to office hours and we will discuss this