The best solution I found so far (posted here) is:

• In MMA10 export the notebook as CDF (File - CDF Export). Let's say you call it test.cdf and save it in D:\
• Close the CDF File and, always In MMA 10, open a new notebook (or use an existing one) and paste the code:

cdf = Import["D:\\test.cdf"];
Delete[cdf, Most@Flatten@Position[cdf, UndoTrackedVariables]];
Export["D:\\test_v9.cdf", %]

• After that you should have a new CDF file (named test_9.cdf and created in D:), compatible with the CDF Player v.9, that shouldn't give you anymore any error message.

As for the next update of the CDF Player (to a version compatible with MMA10), it should happen soon, at least according to the last post in this thread

This beeping is normally displayed when we are dealing with different versions, and it does not means that there is something wrong, but it is just a warning about that some functionality can be missed. However, the fact that there is not CDF Player for Mathematica 10 implies that even the best approach to solve the problem will have to deal with this beeping.

Nevertheless, I agree with you, for readers it immediately throws a cloud of doubt over the entire document. But it is out of our will, it is an issue for Wolfram's guys!

Please!!!!!!!!

Need to deploy to my boss.

But can't.

UndoTrackedVariables is an option associated with the new Undo/Redo functionality in version 10. When you execute a Manipulate command, the resulting internals of the Cell that displays the Manipulate has in it the UndoTrackedVariables option. This is what the version 9 CDFPlayer is generating an error mesage for,

For example, the following Manipulate

Manipulate[x, {x, 1, 2}]

has as its output cell expression

Cell[BoxData[
   TagBox[
     StyleBox[
       DynamicModuleBox[{$CellContext`x$$ = 1, Typeset`show$$ = True, 
      Typeset`bookmarkList$$ = {}, 
          Typeset`bookmarkMode$$ = "Menu", Typeset`animator$$, 
      Typeset`animvar$$ = 1, Typeset`name$$ = 
           "\"untitled\"", Typeset`specs$$ = {{
               Hold[$CellContext`x$$], 1, 2}}, 
      Typeset`size$$ = {8., {0., 9.}}, Typeset`update$$ = 0, 
          Typeset`initDone$$, 
      Typeset`skipInitDone$$ = True, $CellContext`x$2065$$ = 0}, 
         DynamicBox[Manipulate`ManipulateBoxes[
            1, StandardForm, "Variables" :> {$CellContext`x$$ = 1}, 
       "ControllerVariables" :> {
                 Hold[$CellContext`x$$, $CellContext`x$2065$$, 0]}, 
             "OtherVariables" :> {
                Typeset`show$$, Typeset`bookmarkList$$, 
         Typeset`bookmarkMode$$, Typeset`animator$$, 
                 Typeset`animvar$$, Typeset`name$$, Typeset`specs$$, 
         Typeset`size$$, Typeset`update$$, 
                 Typeset`initDone$$, Typeset`skipInitDone$$}, 
       "Body" :> $CellContext`x$$, 
             "Specifications" :> {{$CellContext`x$$, 1, 2}}, 
       "Options" :> {}, "DefaultOptions" :> {}],
           ImageSizeCache -> {247., {49., 54.}},
           SingleEvaluation -> True],
         Deinitialization :> None,
         DynamicModuleValues :> {},
         SynchronousInitialization -> True,
         UndoTrackedVariables :> {Typeset`show$$, 
       Typeset`bookmarkMode$$},
         UnsavedVariables :> {Typeset`initDone$$},
         UntrackedVariables :> {Typeset`size$$}], "Manipulate",
       Deployed -> True,
       StripOnInput -> False],
     Manipulate`InterpretManipulate[1]]], "Output"]