When a user accesses a published Citrix Desktop via web interface, there is a chance they launch two desktops even though the allowed limit is set to one. Due to the user double clicking the published desktop icon quickly they may bypass the limit whilst Citrix Xenapp catches up.
Users rapidly clicking on published application icons can initiate multiple sessions prior to the application instance counter getting updated.
There are two articles from Citrix which resolve this issue. See links below:
http://support.citrix.com/article/CTX118656 (The registry fix here will only work with published apps.)