Since not all instance waits have a query associated with them, the instance waits chart may have more waits than the query waits chart. In addition, even when a wait is both an instance wait and a query wait, the point in time where the wait shows up in the chart may be different. This is because of the way instance waits and query waits are stored in SQL Server's system views. Instance waits are assigned to the point in time when the wait was finished, whereas query waits are recorded in near real-time (and processed by SQL Governor every 100 milliseconds) and assigned to the point in time when they were processed.
For example, a SQL Server Agent job that causes waits at 12:04, 12:06 and 12:08 and finishes at 12:10 will have all its instance waits show up as a spike in the chart at 12:10, but the query wait chart will have three spikes at 12:04, 12:06 and 12:08.