I think the issue is that you are plotting your bars twice. Your legend applies to the data in the order it was plotted, so the first legend entry is applied to the first bar plot, where everything is blue. Then entries 2-4 apply to the first 3 bar plots created in the for loop - red, green and blue.
Since your for loop approach is all you need, remove the first bar command from your code. Try something like this.
% data_kind2=xlsread('kind2.xlsx');
data_kind2 = randi(15,[1,96]);
colors={'r','g','b','k'};
figure();
for ii=0:3
bar(ii*24+(1:24),data_kind2(ii*24+(1:24)),'FaceColor',colors{ii+1})
hold on
end
hold off
legend('Summer','Autumn','Winter','Spring');
set(gca,'Xtick',1:1:96,'XTickLabel',{'Evapotranspiration Deforestation Areas','Evapotranspiration Forest Areas','Evapotranspiration Transition Areas',...
'Soil moisture Deforestation Areas','Soil moisture Forest Areas','Soil moisture Transition Areas',...
'Air Temperature Deforestation Areas','Air Temperature Forest Areas','Air Temperature Transition Areas',...
'Total Runoff Deforestation Areas','Total Runoff Forest Areas','Total Runoff Transition Areas',...
'Sensible Heat Flux Deforestation Areas','Sensible Heat Flux Forest Areas','Sensible Heat Flux Transition Areas',...
'Soil Temperature Deforestation Areas','Soil Temperature Forest Areas','Soil Temperature Transition Areas',...
'ET/P Deforestation Areas','ET/P Forest Areas','ET/P Transition Areas','R/P Deforestation Areas','R/P Forest Areas','R/P Transition Areas',...
'Evapotranspiration Deforestation Areas','Evapotranspiration Forest Areas','Evapotranspiration Transition Areas',...
'Soil moisture Deforestation Areas','Soil moisture Forest Areas','Soil moisture Transition Areas',...
'Air Temperature Deforestation Areas','Air Temperature Forest Areas','Air Temperature Transition Areas',...
'Total Runoff Deforestation Areas','Total Runoff Forest Areas','Total Runoff Transition Areas',...
'Sensible Heat Flux Deforestation Areas','Sensible Heat Flux Forest Areas','Sensible Heat Flux Transition Areas',...
'Soil Temperature Deforestation Areas','Soil Temperature Forest Areas','Soil Temperature Transition Areas',...
'ET/P Deforestation Areas','ET/P Forest Areas','ET/P Transition Areas','R/P Deforestation Areas','R/P Forest Areas','R/P Transition Areas' 'Evapotranspiration Deforestation Areas','Evapotranspiration Forest Areas','Evapotranspiration Transition Areas',...
'Soil moisture Deforestation Areas','Soil moisture Forest Areas','Soil moisture Transition Areas',...
'Air Temperature Deforestation Areas','Air Temperature Forest Areas','Air Temperature Transition Areas',...
'Total Runoff Deforestation Areas','Total Runoff Forest Areas','Total Runoff Transition Areas',...
'Sensible Heat Flux Deforestation Areas','Sensible Heat Flux Forest Areas','Sensible Heat Flux Transition Areas',...
'Soil Temperature Deforestation Areas','Soil Temperature Forest Areas','Soil Temperature Transition Areas',...
'ET/P Deforestation Areas','ET/P Forest Areas','ET/P Transition Areas','R/P Deforestation Areas','R/P Forest Areas','R/P Transition Areas' 'Evapotranspiration Deforestation Areas','Evapotranspiration Forest Areas','Evapotranspiration Transition Areas',...
'Soil moisture Deforestation Areas','Soil moisture Forest Areas','Soil moisture Transition Areas',...
'Air Temperature Deforestation Areas','Air Temperature Forest Areas','Air Temperature Transition Areas',...
'Total Runoff Deforestation Areas','Total Runoff Forest Areas','Total Runoff Transition Areas',...
'Sensible Heat Flux Deforestation Areas','Sensible Heat Flux Forest Areas','Sensible Heat Flux Transition Areas',...
'Soil Temperature Deforestation Areas','Soil Temperature Forest Areas','Soil Temperature Transition Areas',...
'ET/P Deforestation Areas','ET/P Forest Areas','ET/P Transition Areas','R/P Deforestation Areas','R/P Forest Areas','R/P Transition Areas'});
set(gca,'XTickLabelRotation',90)
title('Relative Change v.s Monthly water balance in Deforestation,Forest, and Transition areas');
ylabel('Relative Change <%>')
xlabel('Monthly water balance');
grid on
