It's hard to say for sure what the problem is without the data, but one problem might be that the axes Y-Limits are outside where the rectangles are. The rectangles are all from y=0 to y=1, but the axes Y-Limits may be something else.
For example, with the made up data below, wcoherence creates an axes whose Y-Limits are approximately [-5.19, -1.44] (in spite of the fact that the y-tick labels suggest the Y-Limits are approximately [0.03, 0.3]).
To fix that problem, use the actual Y-Limits as the upper and lower limits of the rectangles. One way to do that is shown below. (I also included a FaceAlpha of 0.5 in the rectangles because otherwise they had no transparency.)
data1 = rand(100,1);
data2 = rand(100,1);
onsetsWC = [20;30;50;80];
durationsWC = [5;7.5;3;10];
Trialtype = {'Chase';'Follow';'Chase';'Follow'};
dataTable = table(onsetsWC,durationsWC,Trialtype);
wcoherence(data1,data2)
ax = gca;
ax.YLim % YLim is not what you might expect from looking at the plot
final_onset = dataTable.onsetsWC(end);
final_duration = dataTable.durationsWC(end);
max_x_limit = final_onset + final_duration;
xlim([0, max_x_limit]);
% use the actual axes YLim in defining the rectangles
y_lim = ax.YLim;
dy_lim = y_lim(2)-y_lim(1);
for i = 1:height(dataTable)
onset = dataTable.onsetsWC(i);
duration = dataTable.durationsWC(i);
trialType = dataTable.Trialtype(i);
if strcmp(trialType, 'Chase')
barColor = [1, 0, 0, 1];
elseif strcmp(trialType, 'Follow')
barColor = [0, 1, 0, 1];
end
rectangle(ax, 'Position', [onset, y_lim(1), duration, dy_lim], ...
'FaceColor', barColor, 'EdgeColor', 'none', 'FaceAlpha', 0.5);
end
