When trying apt-get upgrade, indeed updates are available.
Interesting behavior of Discover: when sudo apt-get upgrade is running in the background launched from konsole, then suddenly Discover show all the updates available, even when before was showing none (and applet was saying there are updates). So I guess it is somehow connected to the Discover caching mechanism or similar.
Can you please indicate which version and distribution you're using?
Kubuntu Linux 4.7.0-040700-generic #201607241632 SMP Sun Jul 24 20:34:30 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Description: Ubuntu 16.10 Release: 16.10 Codename: yakkety
Discover v5.7.5 Using: KDE Frameworks 5.26.0 Qt 5.6.1 (built against 5.6.1) The xcb windowing system
Please update to 5.8 LTS or 5.9 where this is fixed.
*** Bug 375397 has been marked as a duplicate of this bug. ***