subplot creates a cartesian axes in the current position. Since you call geobasemap and geolimits before geoscatter, they attemp to operate on the cartesian axes, which is not allowed.
Try changing the order of your code so that you call geoscatter first, which does create a geographic axes, and then geolimits and geobasemap
subplot(1,2,2)
lat = [42.3501 42.3598 42.3626 42.3668 42.3557];
lon = [-71.0870 -71.0662 -71.0789 -71.0801 -71.0662];
geoscatter(lat,lon,"filled")
geolimits([42.3456 42.3694],[-71.0930 -71.0536])
geobasemap grayterrain
clim([0, 80]);
colorbar;
