This is beacause the duplicated value is being used as a dimension, so it is being "grouped". There are three options when this happens:
1) Leave it grouped! The values would yield the same result, and if you were to click on the point in the chart, those two items would be selected. You'd need to make sure, however that any ranking functions, or other aggregated calculations, sums etc take into account the fact that there are two values. You can set the Qlikview rank() function to return the same rank when two items have the same value.
2) Add a second dimension into the line chart that has a unique value for every x. This will separate them out
3) Use a scatterplot, not a line chart to produce the charts