Issue Tracking Systems (ITSs) enable software developers and managers to collect and resolve issues collaboratively. While researchers have extensively analysed ITS data to automate or assist specific activities such as issue assignments, duplicate detection, or priority prediction, developer studies on ITSs remain rare. Particularly, little is known about the challenges Software Engineering (SE) teams encounter in ITSs and when certain practices and workarounds (such as leaving issue fields like "priority" empty) are considered problematic. To fill this gap, we conducted an in-depth interview study with 26 experienced SE practitioners from different organisations and industries. We asked them about general problems encountered, as well as the relevance of 31 ITS smells (aka potentially problematic practices) discussed in the literature. By applying Thematic Analysis to the interview notes, we identified 14 common problems including issue findability, zombie issues, workflow bloat, and lack of workflow enforcement. Participants also stated that many of the ITS smells do not occur or are not problematic. Our results suggest that ITS problems and smells are highly dependent on context factors such as ITS configuration, workflow stage, and team size. We also discuss potential tooling solutions to configure, monitor, and visualise ITS smells to cope with these challenges.