having 'Measure' > 0 syntax does not work in mdx query
You put the HAVING clause in the ON COLUMNS axis (or ON 0) which attempts to filter out any column which has a null or zero IndentCount. Instead you need to move it to the ON ROWS axis (or ON 1) if you want it eliminate some rows. 

I would also suggest you may optimize the performance by using the NonEmpty function instead of HAVING. Since you can’t have a zero or negative IndentCount the following will do what you want and will perform better since it will only calculate the TOTAL measure for rows you will end up keeping. 

with member [Measures].[TOTAL] AS
SUM(Periodstodate([DimTime].[Year].[(All)] ,[DimTime].[Year].currentmember)
,[Measures].[IndentCount])

Select {[Measures].[IndentCount],[Measures].[TOTAL]}  
   on 0 , 
   NonEmpty([DimTime].[Year].[Year], [Measures].[IndentCount]) on 1
from [Procurement]