I am also seeing this issue both on 10.10.5 and 10.11.1 with Server 5.0.4.
Something interesting that I found in the swupdate settings (by running /Applications/Server.app/Contents/ServerRoot/usr/sbin/serveradmin fullstatus swupdate):
swupdate:state = "RUNNING"
swupdate:lastChecktime = 2015-11-02 21:30:05 +0000
swupdate:autoMirrorOnlyNew = no
swupdate:syncServiceState = "RUNNING"
swupdate:startTime = 2015-11-03 15:38:26 +0000
swupdate:lastProductsUpdate = 2015-11-03 15:37:56 +0000
swupdate:logPaths:swupdateServiceLog = "/Library/Server/Software Update/Log/swupd_syncd.log"
swupdate:logPaths:swupdateErrorLog = "/Library/Server/Software Update/Log/swupd_error.log"
swupdate:logPaths:swupdateAccessLog = "/Library/Server/Software Update/Log/swupd_access.log"
swupdate:pluginVers = "10.11.111 (111)"
swupdate:checkError = no
swupdate:autoEnable = no
swupdate:updatesDocRoot = "/Library/Server/Software Update/Data/"
swupdate:hostServiceState = "RUNNING"
swupdate:autoMirror = yes
swupdate:numOfEnabledPkg = 1011
swupdate:servicePortsAreRestricted = "NO"
swupdate:numOfMirroredPkg = 1207
swupdate:setStateVersion = 1
swupdate:syncStatus = "DONE"
swupdate:readWriteSettingsVersion = 1
I have enabled all but two updates in the GUI, so the enabled count should be 1205, not 1011. That is very strange! Bug report submitted!