Unclear or unknown Definition of Done: Unless all members of the team have the same understanding of when a task is done (and ultimately a PBI), there will always be a reverse flow present on your Sprint board. So, delays, frustration, and missed deadlines will follow.
The Scrum Guide defines the Definition of Done as the transparency needed to define when it's done and make this information known to all on the team, meaning to keep a written note on this in a visually reachable place, like next to the Sprint board or that spot right above the coffee machine you're all staring at while waiting for coffee. Or in Jira?
Wrong Understanding of Timeboxing: Scrum recommends teams to follow timeboxed iterations to software development also known a sprint. Everything within the Sprint has an allocated time, and you are expected to deliver things within this timeframe.
Timeboxing raises your awareness of time, it forces you to practice estimating, and over time it improves your estimation skills. Finally, since time and cost are so tightly coupled, timeboxing allows you to implicitly think about the value you are adding, ultimately managing your risks and scope creep. The idea isn't to put a time-frame on something, but to make the work of a size that will suit the normal, accepted, and currently used timebox. Timeboxing improves focus which results in increase in productivity. Timeboxing helps in team and stakeholders with realization of time in hand and time spent.
Testing Too Late: It seems to be a hallmark of teams fairly new to Agile who tend to bring their previous methods on board. Efficient testing and quick bug turnaround are crucial to making Agile work in at least a basic fashion. Reserve time to think about automate testing and automate runways and execute a strict testing and deployment policy.
No Communication in teams and between teams: Miscommunication is often attributed to distributed teams, but communication can suffer in all circumstances. All it takes is having bad examples set and no training (or common sense) in how much impact this creates to all productivity. Whether your team is spread across different locations in one country or sitting in the same building or rooms, not being able to share thoughts, get feedback on ideas and the common way of working is a common issue. As often mentioned, the best way still is genuine face to face communication, and in making concise agreements about how and what and why. It might be a good idea to create a committed protocol. State clearly what action requires which communicative reaction. It will be hard at first, but people get used to this after a while and information starts to flow beautifully through the team, its direct environment and the whole company.