The options to the v3 Sencha Cmd will be sensitive to ordering. Commands in v3 are processed hierarchically, so options to a particular sub command will need to follow that sub command on the command line.
In this case, the compressor setting (closure or yui) is an option on the concat command, which means it will need to follow that command on the command line.
In the command you show, they are transposed, which would cause this issue, as the higher level compile command does not have options for closure or yui.
This should correct it:
/Users/knalli/bin/Sencha/Cmd/188.8.131.52/sencha compile -classpath=app.js,ext-4.1.1/src,ext-4.1.1/examples/ux,plugins,myappdir exclude -namespace=Ext.chart and concat -out all-classes-dev.js and -debug=false concat -out all-classes-debug.js and concat -closure -out=all-classes-prod.js