The field of glottochronology has yet to be proved on its scientific rigor due to the underlying assumptions oversimplifying the complexities of languages.
The rate of loss of basic vocabulary items is assumed to be the same for all languages
The rate of rentention of  basic vocabulary items is assumed to be constant over time
However the comparative method is not without flaws, or criticism: Ironically these issues fall into the camp of the comparative method being too similar to genetics, and issues caused by the comparative method not being similar enough.
In the former camp, many modern day linguists consider the tree model implied by the comparative method as overly simplistic, and express doubts that genealogical comparison like is misleading. A tree model implies a series of distinct nodes: It implies sudden and irrevocable change in a population preventing further contact ie many different proto-languages coexisting without further interaction, which is clearly misleading in areas of continuous landmass. Critics claim the model ignores situations where many dialects within a language evolve into distinct languages, over a long period of time where innovations are shared (known as areal diffusion). Populations bordering others have a higher borrowing of linguistic features of each other, as well as similar cultures - influencing linguistic change in a shared direction, this is known as linkage. Different models such as the wave model, which attempts to describe how language features spread over a continuous territory, and are gaining popularity with modern linguists as a way of modelling linguistic linkage and areal diffusion. A good analogy is of a pebble thrown into a pond, the effect is strongest near the epicentre, and weakens as it radially spreads. 
Another problem picturing languages as distinct nodes is the idea of linguistic uniformity within a proto-language, despite the existence of dialects within even small language communities (However the real life implications of this simplification are doubted) \cite{campbell2004}.  
The other main issues with the comparative method come from an underlying assumption that sounds will evolve in a fixed way; despite the reality that linguistic change is far more random and shares a lot of issues with genetics. A good example being analogy, where words of separate and unrelated languages coincidentally converge implying false relatedness. Words and linguistic features are often borrowed from other languages, which can imply a closer degree of relatedness that is correct.  

Genetic linguistic research methods

Biologists have leaned into the similarities between linguistics and genetics and used algorithms used in genetic phylogeny to create deep tim. As with genes, and contrary to historical comparative method thinking, words are gained and lost  Evolutionary models can take into account areal diffusion (horizontal transmission) 

Bayesian Phylogenetics

Modern day linguistical phylogenetic methods are usually based on Bayesian Markov Chain Monte Carlo (MCMC) methods, the full depth of these methods is beyond the scope of this paper, but we can establish the foundations of the method, and how it can be applied to phylogenetics.

An Introduction to Bayes' theorem

To explain it we will start with Bayes' theorem: