Unexpected price values in Quotes or Invoices are likely due to a Fee Matrix and Custom Row setup that has since been disabled.
The unfortunate side-effect of this is that those values and settings can remain in old Project Elements (i.e., Quotes, Invoices, etc.) and will propagate if the Element is copied.
The first step to confirming this is to go to Financials-->Fee Matrices to see if any have been created. Flex does not have any Fee Matrices set up by default, so there only be results in this screen if a User has created one. Make a note of all entries in the Name column.
Next, go to Projects-->Project Elements, choose the Element for which you're experiencing issues, then go to its Custom Rows tab. Flex does have several "default" Custom Rows for certain Project Elements. However, the defaults are likely named something much different than the Fee Matrices located in the first step. You can double-click any of the entries here to see its settings. You'll need to locate any that use the Fee Matrices located in the first step and make a note of their Code.
The next step is to flip over to the Document Views tab and select a view which you can safely edit. In most cases, this is a temporary issue, so editing the Working View is recommended. If the issue is widespread and on-going, you may want to edit Profit / Markup or create an entirely new view (that process is covered in our Best Practices - Document Views webinar).
Once you've selected a view, go to its Total Block Rows section. Enter a caption in the field provided, choose _Custom Row_ from the first drop-down, then find the Code for the Custom Row in question in the second drop-down under the Custom Row column, then click the big green plus button to add the row. Its placement doesn't matter for this exercise, but the list can be reordered via drag & drop. Click UPDATE to commit the changes.
The final step is to locate your problem Element again and reload it. Check its Totals & Notes section for the changes that were just made. Assuming you found the problem Row, you can click on the value on the right side of the Total Block grid and enter $0.00 to remove the value.
If you did not select the problem Row on the first try, flip back to the Element's settings, edit the same Document View, and change the selected Code for the Custom Row you just created. Click UPDATE and reload the Element. Repeat until you've located the problem Row.
Once located, you can clear the value as needed, change the Document View on which it appears, etc. It's also a recommend practice to caption the Total Block Row in such a way that Users know it should not be used.