Despite the fact that fluorescence induction is a very complicated process, the technique is used to obtain information regarding connectivity in photosynthetic systems. The models generally used for the analysis are oversimplified, which in some cases has led to questionable interpretations. Here we describe the effects of nonlinear loss processes in (pulsed) induction experiments and how they obscure the features attributed to large-scale connectivity in chloroplasts. We simulate the fluorescence induction process for finite size domains (1-4 reaction centers per domain) and describe both the trapping process and the generation of triplets by a discrete state model. From our numerical calculations it is demonstrated that singlet-triplet annihilation is unavoidable when using microsecond pulses for actinic illumination.