Can someone explain to me what the 1s catching problem is in the Master Slave Flip Flop?
When you set or reset the flip flop the results of that set or reset are seen only when the clock signal transitions from a HIGH to a LOW level (known as a "falling edge").  This can be seen at about 80ns where the falling Q coincides with the falling C.

When you set S it first sets Y before it propagates out to Q on a falling C.  When you set R it resets Y, which then propagates out to Q on the falling C.

If Y is set and then immediately reset before the next falling C the change in Y will never be reflected in Q.  So if you set S and then, before the following falling C set R, the output Q will never change, so those two events of setting and resetting are "lost" in the internals of the flip-flop, and you never know they have happened.

In the waveform you have, Y would have to be HIGH at 140ns in order for Q to react to the S at ~125ns, but the R at ~130ns has cancelled it out before you could see it.