This is odd. It really looks like a Bug... partly
The reason is probably that the angle of the lines are so narrow that MATLAB runs into rounding errors when calculating the points to draw for your limits very small limits given very large numbers. (You see that you don't run into this problem when you don't scale the matrix mgc.
mgc = randi([-900*10^10,900*10^10], [1000,2]);
plot(mgc(:,1),mgc(:,2))
ylim([-1,1])
but if you scale it further, you run into this problem...
mgc = randi([-900*10^10,900*10^10], [1000,2]);
plot(mgc(:,1)*1e6,mgc(:,2)*1e6)
ylim([-1,1])

While those numbers are nowhere near the maximum number a double can represent (type realmax in the command window to see that this is a number with 308 zeros!); limiting the plot to [-1,1] on one of the axes -- note that you obtain the same phenom on the x-axis -- let MATLAB run into precision problems.
First of all, you see that it plots much less lines than before (in my case)... although, I just said to zoom on the y-axis. The thing is, that MATLAB does not recalculate the lines for the section but it really zooms into it (I guess that this may cause resolution errors with regard to pixels?)
Well, lets have a look at the data (Pro-tip, you can get the data of a line from a MATLAB figure by calling this snippet
datObj = findobj(gcf,'-property','YData','-property','XData');
X = datObj.XData;
Y = datObj.YData;
xlm = get(gca,'XLim'); % get the current x-limits
) We see that it represents the original data set, which is not surprising as you can also zoom out again.
Note that his only occurs if you have such a chaotic, jagged line. If you sort it, it does not happen.
quick fix:
Now, what happens, if we calculate the exact points for this section?
m = diff(Y)./diff(X); % slope
n = Y(1:end-1)-m.*X(1:end-1); % offset
x = [(-1-n); (1-n)]./m;
y = ones(size(x))./[-1 1].';
% plot
plot([xMinus1;xPlus1],(ones(length(xMinus1),2).*[-1 1]).')
xlim(xlm); % limit to exact same scale as before

The different colors indicate that they are now individual lines and not a single wild chaos;)