I can't tell without seeing your data, but I'm guessing that your dates are in a format that OGS doesn't understand (which is basically anything but decimal numbers) and when we import your points, we're replacing your x values with 1,2,3... and using the x column as custom axis labels. You can check this in the data inspector.
If that's the case, then when you import the second half of your data, we start over at 1 and you get the 2 overlaid series instead of one continuous one. The way around this would be to either import 1 column at a time (first the X values, which would be taken as custom x-axis tick labels, then the y values, which would be plotted against those values) or convert your dates to elapsed time values which OGS can work with. The DATEDIF function in Apple Numbers calculates a number of days from a date value.
I hope this helps - if it doesn't, be sure to Help > Send Feedback within OGS or email
OmniGraphSketcher@omnigroup.com